gap Gap Gap Locations Mapping and Sequencing Description This track depicts gaps in the assembly. There are 154,810 gaps of size 100 bases or more for a total of 98,876,036 bases. The largest gap is 3,000 bases. Gaps are represented as black boxes in this track. If the relative order and orientation of the contigs on either side of the gap is known, it is a bridged gap and a white line is drawn through the black box representing the gap. All gaps in this assembly are bridged fragment gaps: Fragment - gaps between the Whole Genome Shotgun contigs of a supercontig. (In this context, a contig is a set of overlapping sequence reads. A supercontig is a set of contigs ordered and oriented during the Whole Genome Shotgun process using paired-end reads.) These are represented by varying numbers of Ns in the assembly. Fragment gap sizes are usually taken from read pair data. 
mrna Marmoset mRNAs Marmoset mRNAs from GenBank mRNA and EST Description The mRNA track shows alignments between marmoset mRNAs in GenBank and the genome. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality. The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: Type a term in one or more of the text boxes to filter the mRNA display. For example, to apply the filter to all mRNAs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the "tissue" table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter. If filtering on more than one value, choose the desired combination logic. If "and" is selected, only mRNAs that match all filter criteria will be highlighted. If "or" is selected, mRNAs that match any one of the filter criteria will be highlighted. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If "exclude" is chosen, the browser will not display mRNAs that match the filter criteria. If "include" is selected, the browser will display only those mRNAs that match the filter criteria. This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. For more information about this option, go to the Codon and Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page. Methods GenBank marmoset mRNAs were aligned against the genome using the blat program. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept. Credits The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide. References Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
nscanGene N-SCAN N-SCAN Gene Predictions Genes and Gene Predictions Description This track shows gene predictions using the N-SCAN gene structure prediction software provided by the Computational Genomics Lab at Washington University in St. Louis, MO, USA. Methods N-SCAN PASA-EST N-SCAN combines biological-signal modeling in the target genome sequence along with information from a multiple-genome alignment to generate de novo gene predictions. It extends the TWINSCAN target-informant genome pair to allow for an arbitrary number of informant sequences as well as richer models of sequence evolution. N-SCAN models the phylogenetic relationships between the aligned genome sequences, context-dependent substitution rates, insertions, and deletions. For creating predictions on marmoset, N-SCAN uses mouse (mm9) as the informant. N-SCAN PASA-EST combines EST alignments into N-SCAN. Similar to the conservation sequence models in TWINSCAN, separate probability models are developed for EST alignments to genomic sequence in exons, introns, splice sites and UTRs, reflecting the EST alignment patterns in these regions. N-SCAN PASA-EST is more accurate than N-SCAN while retaining the ability to discover novel genes to which no ESTs align. Due to the availability of only a small number of marmoset cDNA sequences, EST sequence evidence was created using UCSC's liftOver program to map PASA-clustered ESTs from human (hg18) to the calJac1 genome. See the description of N-SCAN PASA-EST under hg18 for more details. No manual annotation was performed to generate any of the gene models. The high accuracy of the set is in part due to the large number of available human ESTs and full length cDNAs. Credits Thanks to Michael Brent's Computational Genomics Group at Washington University St. Louis for providing these data. Special thanks for this implementation of N-SCAN to Aaron Tenney in the Brent lab, and Robert Zimmermann, currently at Max F. Perutz Laboratories in Vienna, Austria. References Gross SS, Brent MR. Using multiple alignments to improve gene prediction. J Comput Biol. 2006 Mar;13(2):379-93. PMID: 16597247 Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 2003 Oct 1;31(19):5654-66. PMID: 14500829; PMC: PMC206470 Korf I, Flicek P, Duan D, Brent MR. Integrating genomic homology into gene structure prediction. Bioinformatics. 2001;17 Suppl 1:S140-8. PMID: 11473003 van Baren MJ, Brent MR. Iterative gene prediction and pseudogene removal improves genome annotation. Genome Res. 2006 May;16(5):678-85. PMID: 16651666; PMC: PMC1457044 
rmsk RepeatMasker Repeating Elements by RepeatMasker Variation and Repeats Description This track was created by using Arian Smit's RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences. The program outputs a detailed annotation of the repeats that are present in the query sequence (represented by this track), as well as a modified version of the query sequence in which all the annotated repeats have been masked (generally available on the Downloads page). RepeatMasker uses the Repbase Update library of repeats from the Genetic Information Research Institute (GIRI). Repbase Update is described in Jurka (2000) in the References section below. Some newer assemblies have been made with Dfam, not Repbase. You can find the details for how we make our database data here in our "makeDb/doc/" directory. Display Conventions and Configuration In full display mode, this track displays up to ten different classes of repeats: Short interspersed nuclear elements (SINE), which include ALUs Long interspersed nuclear elements (LINE) Long terminal repeat elements (LTR), which include retroposons DNA repeat elements (DNA) Simple repeats (micro-satellites) Low complexity repeats Satellite repeats RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA) Other repeats, which includes class RC (Rolling Circle) Unknown The level of color shading in the graphical display reflects the amount of base mismatch, base deletion, and base insertion associated with a repeat element. The higher the combined number of these, the lighter the shading. A "?" at the end of the "Family" or "Class" (for example, DNA?) signifies that the curator was unsure of the classification. At some point in the future, either the "?" will be removed or the classification will be changed. Methods Data are generated using the RepeatMasker -s flag. Additional flags may be used for certain organisms. Repeats are soft-masked. Alignments may extend through repeats, but are not permitted to initiate in them. See the FAQ for more information. Credits Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and repeat libraries used to generate this track. References Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010. Repbase Update is described in: Jurka J. Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet. 2000 Sep;16(9):418-420. PMID: 10973072 For a discussion of repeats in mammalian genomes, see: Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999 Dec;9(6):657-63. PMID: 10607616 Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8. PMID: 8994846 
xenoRefGene Other RefSeq Non-Marmoset RefSeq Genes Genes and Gene Predictions Description This track shows known protein-coding and non-protein-coding genes for organisms other than marmoset, taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated weekly. Display Conventions and Configuration This track follows the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), reviewed (dark). The item labels and display colors of features within this track can be configured through the controls at the top of the track description page. Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name instead of the gene name, show both the gene and accession names, or turn off the label completely. Codon coloring: This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page. Hide non-coding genes: By default, both the protein-coding and non-protein-coding genes are displayed. If you wish to see only the coding genes, click this box. Methods The RNAs were aligned against the marmoset genome using blat; those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 25% base identity with the genomic sequence were kept. Credits This track was produced at UCSC from RNA sequence data generated by scientists worldwide and curated by the NCBI RefSeq project. References Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. PMID: 24259432; PMC: PMC3965018 Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979 
intronEst Spliced ESTs Marmoset ESTs That Have Been Spliced mRNA and EST Description This track shows alignments between marmoset expressed sequence tags (ESTs) in GenBank and the genome that show signs of splicing when aligned against the genome. ESTs are single-read sequences, typically about 500 bases in length, that usually represent fragments of transcribed genes. To be considered spliced, an EST must show evidence of at least one canonical intron (i.e., the genomic sequence between EST alignment blocks must be at least 32 bases in length and have GT/AG ends). By requiring splicing, the level of contamination in the EST databases is drastically reduced at the expense of eliminating many genuine 3' ESTs. For a display of all ESTs (including unspliced), see the marmoset EST track. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. In dense display mode, darker shading indicates a larger number of aligned ESTs. The strand information (+/-) indicates the direction of the match between the EST and the matching genomic sequence. It bears no relationship to the direction of transcription of the RNA with which it might be associated. The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: Type a term in one or more of the text boxes to filter the EST display. For example, to apply the filter to all ESTs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the "tissue" table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter. If filtering on more than one value, choose the desired combination logic. If "and" is selected, only ESTs that match all filter criteria will be highlighted. If "or" is selected, ESTs that match any one of the filter criteria will be highlighted. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If "exclude" is chosen, the browser will not display ESTs that match the filter criteria. If "include" is selected, the browser will display only those ESTs that match the filter criteria. This track may also be configured to display base labeling, a feature that allows the user to display all bases in the aligning sequence or only those that differ from the genomic sequence. For more information about this option, go to the Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page. Methods To make an EST, RNA is isolated from cells and reverse transcribed into cDNA. Typically, the cDNA is cloned into a plasmid vector and a read is taken from the 5' and/or 3' primer. For most — but not all — ESTs, the reverse transcription is primed by an oligo-dT, which hybridizes with the poly-A tail of mature mRNA. The reverse transcriptase may or may not make it to the 5' end of the mRNA, which may or may not be degraded. In general, the 3' ESTs mark the end of transcription reasonably well, but the 5' ESTs may end at any point within the transcript. Some of the newer cap-selected libraries cover transcription start reasonably well. Before the cap-selection techniques emerged, some projects used random rather than poly-A priming in an attempt to retrieve sequence distant from the 3' end. These projects were successful at this, but as a side effect also deposited sequences from unprocessed mRNA and perhaps even genomic sequences into the EST databases. Even outside of the random-primed projects, there is a degree of non-mRNA contamination. Because of this, a single unspliced EST should be viewed with considerable skepticism. To generate this track, marmoset ESTs from GenBank were aligned against the genome using blat. Note that the maximum intron length allowed by blat is 750,000 bases, which may eliminate some ESTs with very long introns that might otherwise align. When a single EST aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence are displayed in this track. Credits This track was produced at UCSC from EST sequence data submitted to the international public sequence databases by scientists worldwide. References Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
refGene RefSeq Genes RefSeq Genes Genes and Gene Predictions Description The RefSeq Genes track shows known marmoset protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated weekly. Please visit the Feedback for Gene and Reference Sequences (RefSeq) page to make suggestions, submit additions and corrections, or ask for help concerning RefSeq records. For more information on the different gene tracks, see our Genes FAQ. Display Conventions and Configuration This track follows the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), reviewed (dark). The item labels and display colors of features within this track can be configured through the controls at the top of the track description page. Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name instead of the gene name, show both the gene and accession names, or turn off the label completely. Codon coloring: This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page. Hide non-coding genes: By default, both the protein-coding and non-protein-coding genes are displayed. If you wish to see only the coding genes, click this box. Methods RefSeq RNAs were aligned against the marmoset genome using BLAT. Those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept. Credits This track was produced at UCSC from RNA sequence data generated by scientists worldwide and curated by the NCBI RefSeq project. References Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. PMID: 24259432; PMC: PMC3965018 Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979 
gold Assembly Assembly from Fragments Mapping and Sequencing Description This track shows the draft assembly of the marmoset genome. This is a 6X coverage assembly. There are 49,724 supercontigs with a total of 3,029,401,840 bases. The largest contig is Contig1, with a size of 2,551,648 bases. Half of the sequence is contained in the 2,807 largest contigs of size 303,219 bases (N50) or larger. The average contig size is 60,924 bases, the median contig size is 8,789 bases. See also: WUSTL Callithrix jacchus assembly details. Whole-genome shotgun reads were assembled into contigs. When possible, contigs were grouped into scaffolds (also known as "supercontigs"). The order, orientation and gap sizes between contigs within a scaffold are based on paired-end read evidence. In dense mode, this track depicts the contigs that make up the currently viewed scaffold. Contig boundaries are distinguished by the use of alternating gold and brown coloration. Where gaps exist between contigs, spaces are shown between the gold and brown blocks. The relative order and orientation of the contigs within a scaffold is always known; therefore, a line is drawn in the graphical display to bridge the blocks. All components within this track are of fragment type "W": Whole Genome Shotgun contig. 
augustusGene AUGUSTUS AUGUSTUS ab initio gene predictions v3.1 Genes and Gene Predictions Description This track shows ab initio predictions from the program AUGUSTUS (version 3.1). The predictions are based on the genome sequence alone. For more information on the different gene tracks, see our Genes FAQ. Methods Statistical signal models were built for splice sites, branch-point patterns, translation start sites, and the poly-A signal. Furthermore, models were built for the sequence content of protein-coding and non-coding regions as well as for the length distributions of different exon and intron types. Detailed descriptions of most of these different models can be found in Mario Stanke's dissertation. This track shows the most likely gene structure according to a Semi-Markov Conditional Random Field model. Alternative splicing transcripts were obtained with a sampling algorithm (--alternatives-from-sampling=true --sample=100 --minexonintronprob=0.2 --minmeanexonintronprob=0.5 --maxtracks=3 --temperature=2). The different models used by Augustus were trained on a number of different species-specific gene sets, which included 1000-2000 training gene structures. The --species option allows one to choose the species used for training the models. Different training species were used for the --species option when generating these predictions for different groups of assemblies. Assembly Group Training Species Fish zebrafish Birds chicken Human and all other vertebrates human Nematodes caenorhabditis Drosophila fly A. mellifera honeybee1 A. gambiae culex S. cerevisiae saccharomyces This table describes which training species was used for a particular group of assemblies. When available, the closest related training species was used. Credits Thanks to the Stanke lab for providing the AUGUSTUS program. The training for the chicken version was done by Stefanie König and the training for the human and zebrafish versions was done by Mario Stanke. References Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656 Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25. PMID: 14534192 
gc5Base GC Percent GC Percent in 5-Base Windows Mapping and Sequencing Description The GC percent track shows the percentage of G (guanine) and C (cytosine) bases in 5-base windows. High GC content is typically associated with gene-rich areas. This track may be configured in a variety of ways to highlight different apsects of the displayed information. Click the "Graph configuration help" link for an explanation of the configuration options. Credits The data and presentation of this graph were prepared by Hiram Clawson. 
genscan Genscan Genes Genscan Gene Predictions Genes and Gene Predictions Description This track shows predictions from the Genscan program written by Chris Burge. The predictions are based on transcriptional, translational and donor/acceptor splicing signals as well as the length and compositional distributions of exons, introns and intergenic regions. For more information on the different gene tracks, see our Genes FAQ. Display Conventions and Configuration This track follows the display conventions for gene prediction tracks. The track description page offers the following filter and configuration options: Color track by codons: Select the genomic codons option to color and label each codon in a zoomed-in display to facilitate validation and comparison of gene predictions. Go to the Coloring Gene Predictions and Annotations by Codon page for more information about this feature. Methods For a description of the Genscan program and the model that underlies it, refer to Burge and Karlin (1997) in the References section below. The splice site models used are described in more detail in Burge (1998) below. Credits Thanks to Chris Burge for providing the Genscan program. References Burge C. Modeling Dependencies in Pre-mRNA Splicing Signals. In: Salzberg S, Searls D, Kasif S, editors. Computational Methods in Molecular Biology. Amsterdam: Elsevier Science; 1998. p. 127-163. Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 1997 Apr 25;268(1):78-94. PMID: 9149143 
est Marmoset ESTs Marmoset ESTs Including Unspliced mRNA and EST Description This track shows alignments between marmoset expressed sequence tags (ESTs) in GenBank and the genome. ESTs are single-read sequences, typically about 500 bases in length, that usually represent fragments of transcribed genes. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality. The strand information (+/-) indicates the direction of the match between the EST and the matching genomic sequence. It bears no relationship to the direction of transcription of the RNA with which it might be associated. The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: Type a term in one or more of the text boxes to filter the EST display. For example, to apply the filter to all ESTs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the "tissue" table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter. If filtering on more than one value, choose the desired combination logic. If "and" is selected, only ESTs that match all filter criteria will be highlighted. If "or" is selected, ESTs that match any one of the filter criteria will be highlighted. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If "exclude" is chosen, the browser will not display ESTs that match the filter criteria. If "include" is selected, the browser will display only those ESTs that match the filter criteria. This track may also be configured to display base labeling, a feature that allows the user to display all bases in the aligning sequence or only those that differ from the genomic sequence. For more information about this option, go to the Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page. Methods To make an EST, RNA is isolated from cells and reverse transcribed into cDNA. Typically, the cDNA is cloned into a plasmid vector and a read is taken from the 5' and/or 3' primer. For most — but not all — ESTs, the reverse transcription is primed by an oligo-dT, which hybridizes with the poly-A tail of mature mRNA. The reverse transcriptase may or may not make it to the 5' end of the mRNA, which may or may not be degraded. In general, the 3' ESTs mark the end of transcription reasonably well, but the 5' ESTs may end at any point within the transcript. Some of the newer cap-selected libraries cover transcription start reasonably well. Before the cap-selection techniques emerged, some projects used random rather than poly-A priming in an attempt to retrieve sequence distant from the 3' end. These projects were successful at this, but as a side effect also deposited sequences from unprocessed mRNA and perhaps even genomic sequences into the EST databases. Even outside of the random-primed projects, there is a degree of non-mRNA contamination. Because of this, a single unspliced EST should be viewed with considerable skepticism. To generate this track, marmoset ESTs from GenBank were aligned against the genome using blat. Note that the maximum intron length allowed by blat is 750,000 bases, which may eliminate some ESTs with very long introns that might otherwise align. When a single EST aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept. Credits This track was produced at UCSC from EST sequence data submitted to the international public sequence databases by scientists worldwide. References Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
microsat Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats Variation and Repeats Description This track displays regions that are likely to be useful as microsatellite markers. These are sequences of at least 15 perfect di-nucleotide and tri-nucleotide repeats and tend to be highly polymorphic in the population. Methods The data shown in this track are a subset of the Simple Repeats track, selecting only those repeats of period 2 and 3, with 100% identity and no indels and with at least 15 copies of the repeat. The Simple Repeats track is created using the Tandem Repeats Finder. For more information about this program, see Benson (1999). Credits Tandem Repeats Finder was written by Gary Benson. References Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999 Jan 15;27(2):573-80. PMID: 9862982; PMC: PMC148217 
quality Quality Scores Marmoset Sequencing Quality Scores Mapping and Sequencing Description The Quality Scores track shows the sequencing quality score of each base in the assembly. The height at each position of the track indicates the quality of the base. When zoomed out to a large range, the heights reflect the averaged scores. This track may be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options. Credits The quality scores were provided as part of the marmoset assembly. The database representation and graphical display code were written by Hiram Clawson. 
simpleRepeat Simple Repeats Simple Tandem Repeats by TRF Variation and Repeats Description This track displays simple tandem repeats (possibly imperfect repeats) located by Tandem Repeats Finder (TRF) which is specialized for this purpose. These repeats can occur within coding regions of genes and may be quite polymorphic. Repeat expansions are sometimes associated with specific diseases. Methods For more information about the TRF program, see Benson (1999). Credits TRF was written by Gary Benson. References Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999 Jan 15;27(2):573-80. PMID: 9862982; PMC: PMC148217 
cons9way Conservation 9-Way Multiz Alignment & Conservation Comparative Genomics Description This track shows multiple alignments of 9 vertebrate species with a measure of evolutionary conservation, based on a phylogenetic hidden Markov model, phastCons (Siepel et al., 2005). The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. The conservation measurements were created using the phastCons package from Adam Siepel at Cold Spring Harbor Laboratory. Multiz alignments of the following assemblies were used to generate this track: OrganismSpeciesRelease date UCSC versionalignment type MarmosetCallithrix jacchus June 2007calJac1reference species RhesusMacaca mulatta Jan 2006rheMac2reciprocal best net OrangutanPongo pygmaeus abelii July 2007ponAbe2reciprocal best net ChimpanzeePan troglodytes Mar 2006panTro2reciprocal best net HumanHomo sapiens Mar 2006hg18reciprocal best net MouseMus musculus Jul 2007mm9reciprocal best net DogCanis familiaris May 2005canFam2reciprocal best net OpossumMonodelphis domestica Jan 2006monDom4chain net PlatypusOrnithorhychus anatinus Mar 2007ornAna1chain net Table 1. Genome assemblies included in the 9-way Conservation track. Display Conventions and Configuration The track configuration options allow the user to display either the vertebrate or placental mammal conservation scores, or both simultaneously. In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options. Pairwise alignments of each species to the marmoset genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons. Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Note that excluding species from the pairwise display does not alter the the conservation score display. To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment. Gap Annotation The Display chains between alignments configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used: Single line: No bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the marmoset genome or a lineage-specific deletion between the aligned blocks in the aligning species. Double line: Aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species. Pale yellow coloring: Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species. Genomic Breaks Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows: Vertical blue bar: Represents a discontinuity that persists indefinitely on either side, e.g. a large region of DNA on either side of the bar comes from a different chromosome in the aligned species due to a large scale rearrangement. Green square brackets: Enclose shorter alignments consisting of DNA from one genomic context in the aligned species nested inside a larger chain of alignments from a different genomic context. The alignment within the brackets may represent a short misalignment, a lineage-specific insertion of a transposon in the marmoset genome that aligns to a paralogous copy somewhere else in the aligned species, or other similar occurrence. Base Level When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the marmoset sequence at those alignment positions relative to the longest non-marmoset sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+". Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes: No codon translation: The gene annotation is not used; the bases are displayed without translation. Use default species reading frames for translation: The annotations from the genome displayed in the Default species to establish reading frame pull-down menu are used to translate all the aligned species present in the alignment. Use reading frames for species if available, otherwise no translation: Codon translation is performed only for those species where the region is annotated as protein coding. Use reading frames for species if available, otherwise use default species: Codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation. Codon translation uses the following gene tracks as the basis for translation, depending on the species chosen (Table 2). Species listed in the row labeled "None" do not have species-specific reading frames for gene translation. Gene TrackSpecies UCSC Geneshuman, mouse Ensembl Geneschimp, rhesus, opossum, platypus Xeno mRNAsorangutan, marmoset, dog Table 2. Gene tracks used for codon translation. Methods Pairwise alignments with the marmoset genome were generated for each species using blastz from repeat-masked genomic sequence. Pairwise alignments were then linked into chains using a dynamic programming algorithm that finds maximally scoring chains of gapless subsections of the alignments organized in a kd-tree. The scoring matrix and parameters for pairwise alignment and chaining were tuned for each species based on phylogenetic distance from the reference. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net. For more information about the chaining and netting process and parameters for each species, see the description pages for the Chain and Net tracks. An additional filtering step was introduced in the generation of the 9-way conservation track to reduce the number of paralogs and pseudogenes from the high-quality assemblies and the suspect alignments from the low-quality assemblies: the pairwise alignments of high-quality mammalian sequences (placental and marsupial) were filtered based on synteny; those for 2X mammalian genomes were filtered to retain only alignments of best quality in both the target and query ("reciprocal best"). The resulting best-in-genome pairwise alignments were progressively aligned using multiz/autoMZ, following the tree topology diagrammed above, to produce multiple alignments. The multiple alignments were post-processed to add annotations indicating alignment gaps, genomic breaks, and base quality of the component sequences. The annotated multiple alignments, in MAF format, are available for bulk download. An alignment summary table containing an entry for each alignment block in each species was generated to improve track display performance at large scales. Framing tables were constructed to enable visualization of codons in the multiple alignment display. Conservation scoring was performed using the PhastCons package (A. Siepel), which computes conservation based on a two-state phylogenetic hidden Markov model (HMM). PhastCons measurements rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The vertebrate tree model for this track was generated using the phyloFit program from the phastCons package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 28-way human(hg18) alignment (msa_view). The 4d sites were derived from the Oct 2005 Gencode Reference Gene set, which was filtered to select single-coverage long transcripts. The phastCons parameters used for the conservation measurement were: expected-length=45, target-coverage=.3 and rho=.31 The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Unlike many conservation-scoring programs, note that phastCons does not rely on a sliding window of fixed size; therefore, short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. 2005. PhastCons currently treats alignment gaps as missing data, which sometimes has the effect of producing undesirably high conservation scores in gappy regions of the alignment. We are looking at several possible ways of improving the handling of alignment gaps. Credits This track was created using the following programs: Alignment tools: blastz and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC Conservation scoring: PhastCons, phyloFit, tree_doctor, msa_view by Adam Siepel while at UCSC, now at Cold Spring Harbor Laboratory MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC Tree image generator: phyloPng by Galt Barber, UCSC Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC The phylogenetic tree is based on Murphy et al. (2001) and general consensus in the vertebrate phylogeny community as of March 2007. References Phylo-HMMs and phastCons: Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104. PMID: 8583911 Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. PMID: 16024819; PMC: PMC1182216 Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993-1005. PMID: 7713447; PMC: PMC1206396 Chain/Net: Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Multiz: Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. PMID: 15060014; PMC: PMC383317 Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007. Blastz: Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 Phylogenetic Tree: Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001 Dec 14;294(5550):2348-51. PMID: 11743200 
cons9wayViewalign Multiz Alignments 9-Way Multiz Alignment & Conservation Comparative Genomics 
multiz9way Multiz Align Multiz Alignments of 9 Species (5 mammals, 4 primates) Comparative Genomics Description This track shows multiple alignments of 9 vertebrate species with a measure of evolutionary conservation, based on a phylogenetic hidden Markov model, phastCons (Siepel et al., 2005). The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. The conservation measurements were created using the phastCons package from Adam Siepel at Cold Spring Harbor Laboratory. Multiz alignments of the following assemblies were used to generate this track: OrganismSpeciesRelease date UCSC versionalignment type MarmosetCallithrix jacchus June 2007calJac1reference species RhesusMacaca mulatta Jan 2006rheMac2reciprocal best net OrangutanPongo pygmaeus abelii July 2007ponAbe2reciprocal best net ChimpanzeePan troglodytes Mar 2006panTro2reciprocal best net HumanHomo sapiens Mar 2006hg18reciprocal best net MouseMus musculus Jul 2007mm9reciprocal best net DogCanis familiaris May 2005canFam2reciprocal best net OpossumMonodelphis domestica Jan 2006monDom4chain net PlatypusOrnithorhychus anatinus Mar 2007ornAna1chain net Table 1. Genome assemblies included in the 9-way Conservation track. Display Conventions and Configuration The track configuration options allow the user to display either the vertebrate or placental mammal conservation scores, or both simultaneously. In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options. Pairwise alignments of each species to the marmoset genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons. Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Note that excluding species from the pairwise display does not alter the the conservation score display. To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment. Gap Annotation The Display chains between alignments configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used: Single line: No bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the marmoset genome or a lineage-specific deletion between the aligned blocks in the aligning species. Double line: Aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species. Pale yellow coloring: Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species. Genomic Breaks Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows: Vertical blue bar: Represents a discontinuity that persists indefinitely on either side, e.g. a large region of DNA on either side of the bar comes from a different chromosome in the aligned species due to a large scale rearrangement. Green square brackets: Enclose shorter alignments consisting of DNA from one genomic context in the aligned species nested inside a larger chain of alignments from a different genomic context. The alignment within the brackets may represent a short misalignment, a lineage-specific insertion of a transposon in the marmoset genome that aligns to a paralogous copy somewhere else in the aligned species, or other similar occurrence. Base Level When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the marmoset sequence at those alignment positions relative to the longest non-marmoset sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+". Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes: No codon translation: The gene annotation is not used; the bases are displayed without translation. Use default species reading frames for translation: The annotations from the genome displayed in the Default species to establish reading frame pull-down menu are used to translate all the aligned species present in the alignment. Use reading frames for species if available, otherwise no translation: Codon translation is performed only for those species where the region is annotated as protein coding. Use reading frames for species if available, otherwise use default species: Codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation. Codon translation uses the following gene tracks as the basis for translation, depending on the species chosen (Table 2). Species listed in the row labeled "None" do not have species-specific reading frames for gene translation. Gene TrackSpecies UCSC Geneshuman, mouse Ensembl Geneschimp, rhesus, opossum, platypus Xeno mRNAsorangutan, marmoset, dog Table 2. Gene tracks used for codon translation. Methods Pairwise alignments with the marmoset genome were generated for each species using blastz from repeat-masked genomic sequence. Pairwise alignments were then linked into chains using a dynamic programming algorithm that finds maximally scoring chains of gapless subsections of the alignments organized in a kd-tree. The scoring matrix and parameters for pairwise alignment and chaining were tuned for each species based on phylogenetic distance from the reference. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net. For more information about the chaining and netting process and parameters for each species, see the description pages for the Chain and Net tracks. An additional filtering step was introduced in the generation of the 9-way conservation track to reduce the number of paralogs and pseudogenes from the high-quality assemblies and the suspect alignments from the low-quality assemblies: the pairwise alignments of high-quality mammalian sequences (placental and marsupial) were filtered based on synteny; those for 2X mammalian genomes were filtered to retain only alignments of best quality in both the target and query ("reciprocal best"). The resulting best-in-genome pairwise alignments were progressively aligned using multiz/autoMZ, following the tree topology diagrammed above, to produce multiple alignments. The multiple alignments were post-processed to add annotations indicating alignment gaps, genomic breaks, and base quality of the component sequences. The annotated multiple alignments, in MAF format, are available for bulk download. An alignment summary table containing an entry for each alignment block in each species was generated to improve track display performance at large scales. Framing tables were constructed to enable visualization of codons in the multiple alignment display. Conservation scoring was performed using the PhastCons package (A. Siepel), which computes conservation based on a two-state phylogenetic hidden Markov model (HMM). PhastCons measurements rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The vertebrate tree model for this track was generated using the phyloFit program from the phastCons package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 28-way human(hg18) alignment (msa_view). The 4d sites were derived from the Oct 2005 Gencode Reference Gene set, which was filtered to select single-coverage long transcripts. The phastCons parameters used for the conservation measurement were: expected-length=45, target-coverage=.3 and rho=.31 The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Unlike many conservation-scoring programs, note that phastCons does not rely on a sliding window of fixed size; therefore, short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. 2005. PhastCons currently treats alignment gaps as missing data, which sometimes has the effect of producing undesirably high conservation scores in gappy regions of the alignment. We are looking at several possible ways of improving the handling of alignment gaps. Credits This track was created using the following programs: Alignment tools: blastz and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC Conservation scoring: PhastCons, phyloFit, tree_doctor, msa_view by Adam Siepel while at UCSC, now at Cold Spring Harbor Laboratory MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC Tree image generator: phyloPng by Galt Barber, UCSC Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC The phylogenetic tree is based on Murphy et al. (2001) and general consensus in the vertebrate phylogeny community as of March 2007. References Phylo-HMMs and phastCons: Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104. PMID: 8583911 Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. PMID: 16024819; PMC: PMC1182216 Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993-1005. PMID: 7713447; PMC: PMC1206396 Chain/Net: Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Multiz: Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. PMID: 15060014; PMC: PMC383317 Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007. Blastz: Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 Phylogenetic Tree: Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001 Dec 14;294(5550):2348-51. PMID: 11743200 
cons9wayViewphastcons Element Conservation (phastCons) 9-Way Multiz Alignment & Conservation Comparative Genomics 
phastCons9way 9 Species Cons 9 Species (5 mammals, 4 Primates) Conservation by PhastCons Comparative Genomics 
cons9wayViewelements Conserved Elements 9-Way Multiz Alignment & Conservation Comparative Genomics 
phastConsElements9way 9 Species El 9 Species (5 mammals, 4 Primates) Conserved Elements Comparative Genomics Description This track shows predictions of conserved elements produced by the phastCons program. PhastCons is part of the PHAST (PHylogenetic Analysis with Space/Time models) package. The predictions are based on a phylogenetic hidden Markov model (phylo-HMM), a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next. Methods Best-in-genome pairwise alignments were generated for each species using blastz, followed by chaining and netting. A multiple alignment was then constructed from these pairwise alignments using multiz. Predictions of conserved elements were then obtained by running phastCons on the multiple alignments with the --most-conserved option. For more details see the track description for the Conservation track. PhastCons constructs a two-state phylo-HMM with a state for conserved regions and a state for non-conserved regions. The two states share a single phylogenetic model, except that the branch lengths of the tree associated with the conserved state are multiplied by a constant scaling factor rho (0 <= rho <= 1). The free parameters of the phylo-HMM, including the scaling factor rho, are estimated from the data by maximum likelihood using an EM algorithm. This procedure is subject to certain constraints on the "coverage" of the genome by conserved elements and the "smoothness" of the conservation scores. Details can be found in Siepel et al. (2005). The predicted conserved elements are segments of the alignment that are likely to have been "generated" by the conserved state of the phylo-HMM. Each element is assigned a log-odds score equal to its log probability under the conserved model minus its log probability under the non-conserved model. The "score" field associated with this track contains transformed log-odds scores, taking values between 0 and 1000. (The scores are transformed using a monotonic function of the form a * log(x) + b.) The raw log odds scores are retained in the "name" field and can be seen on the details page or in the browser when the track's display mode is set to "pack" or "full". Credits This track was created at UCSC using the following programs: Blastz and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group. AxtBest, axtChain, chainNet, netSyntenic, and netClass by Jim Kent at UCSC. PhastCons by Adam Siepel at Cornell University. References PhastCons Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. Chain/Net Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. Multiz Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007. Blastz Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002;:115-26. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. 
chainNetRheMac2 Rhesus Chain/Net Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both rhesus and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the rhesus assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best rhesus/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The rhesus sequence used in this annotation is from the Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the rhesus/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single rhesus chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of "3000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetRheMac2Viewnet Net Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)), Chain and Net Alignments Comparative Genomics 
netRheMac2 Rhesus Net Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)) Alignment net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both rhesus and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the rhesus assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best rhesus/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The rhesus sequence used in this annotation is from the Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the rhesus/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single rhesus chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of "3000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetRheMac2Viewchain Chain Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)), Chain and Net Alignments Comparative Genomics 
chainRheMac2 Rhesus Chain Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both rhesus and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the rhesus assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best rhesus/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The rhesus sequence used in this annotation is from the Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the rhesus/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single rhesus chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of "3000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetPonAbe2 Orangutan Chain/Net Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both orangutan and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the orangutan assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best orangutan/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The orangutan sequence used in this annotation is from the July 2007 (WUGSC 2.0.2/ponAbe2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the orangutan/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single orangutan chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of "3000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetPonAbe2Viewnet Net Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)), Chain and Net Alignments Comparative Genomics 
netPonAbe2 Orangutan Net Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) Alignment net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both orangutan and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the orangutan assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best orangutan/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The orangutan sequence used in this annotation is from the July 2007 (WUGSC 2.0.2/ponAbe2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the orangutan/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single orangutan chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of "3000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetPonAbe2Viewchain Chain Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)), Chain and Net Alignments Comparative Genomics 
chainPonAbe2 Orangutan Chain Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both orangutan and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the orangutan assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best orangutan/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The orangutan sequence used in this annotation is from the July 2007 (WUGSC 2.0.2/ponAbe2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the orangutan/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single orangutan chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of "3000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetPanTro2 Chimp Chain/Net Chimp (Mar. 2006 (CGSC 2.1/panTro2)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of chimp (Mar. 2006 (CGSC 2.1/panTro2)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both chimp and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the chimp assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best chimp/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The chimp sequence used in this annotation is from the Mar. 2006 (CGSC 2.1/panTro2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the chimp/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single chimp chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of "3000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetPanTro2Viewnet Net Chimp (Mar. 2006 (CGSC 2.1/panTro2)), Chain and Net Alignments Comparative Genomics 
netPanTro2 Chimp Net Chimp (Mar. 2006 (CGSC 2.1/panTro2)) Alignment net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of chimp (Mar. 2006 (CGSC 2.1/panTro2)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both chimp and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the chimp assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best chimp/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The chimp sequence used in this annotation is from the Mar. 2006 (CGSC 2.1/panTro2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the chimp/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single chimp chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of "3000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetPanTro2Viewchain Chain Chimp (Mar. 2006 (CGSC 2.1/panTro2)), Chain and Net Alignments Comparative Genomics 
chainPanTro2 Chimp Chain Chimp (Mar. 2006 (CGSC 2.1/panTro2)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of chimp (Mar. 2006 (CGSC 2.1/panTro2)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both chimp and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the chimp assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best chimp/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The chimp sequence used in this annotation is from the Mar. 2006 (CGSC 2.1/panTro2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the chimp/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single chimp chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of "3000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetHg19 Human Chain/Net Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of human (Feb. 2009 (GRCh37/hg19)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the human assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best human/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The human sequence used in this annotation is from the Feb. 2009 (GRCh37/hg19) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the human/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single human chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A90-330-236-356 C-330100-318-236 G-236-318100-330 T-356-236-33090 Chains scoring below a minimum score of "5000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetHg19Viewnet Net Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments Comparative Genomics 
netHg19 Human Net Human (Feb. 2009 (GRCh37/hg19)) Alignment net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of human (Feb. 2009 (GRCh37/hg19)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the human assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best human/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The human sequence used in this annotation is from the Feb. 2009 (GRCh37/hg19) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the human/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single human chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A90-330-236-356 C-330100-318-236 G-236-318100-330 T-356-236-33090 Chains scoring below a minimum score of "5000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetHg19Viewchain Chain Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments Comparative Genomics 
chainHg19 Human Chain Human (Feb. 2009 (GRCh37/hg19)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of human (Feb. 2009 (GRCh37/hg19)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the human assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best human/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The human sequence used in this annotation is from the Feb. 2009 (GRCh37/hg19) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the human/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single human chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A90-330-236-356 C-330100-318-236 G-236-318100-330 T-356-236-33090 Chains scoring below a minimum score of "5000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetMm9 Mouse Chain/Net Mouse (July 2007 (NCBI37/mm9)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of mouse (July 2007 (NCBI37/mm9)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both mouse and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the mouse assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best mouse/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The mouse sequence used in this annotation is from the July 2007 (NCBI37/mm9) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the mouse/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single mouse chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of "3000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetMm9Viewnet Net Mouse (July 2007 (NCBI37/mm9)), Chain and Net Alignments Comparative Genomics 
netMm9 Mouse Net Mouse (July 2007 (NCBI37/mm9)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of mouse (July 2007 (NCBI37/mm9)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both mouse and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the mouse assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best mouse/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The mouse sequence used in this annotation is from the July 2007 (NCBI37/mm9) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the mouse/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single mouse chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of "3000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetMm9Viewchain Chain Mouse (July 2007 (NCBI37/mm9)), Chain and Net Alignments Comparative Genomics 
chainMm9 Mouse Chain Mouse (July 2007 (NCBI37/mm9)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of mouse (July 2007 (NCBI37/mm9)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both mouse and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the mouse assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best mouse/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The mouse sequence used in this annotation is from the July 2007 (NCBI37/mm9) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the mouse/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single mouse chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of "3000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetCanFam2 Dog Chain/Net Dog (May 2005 (Broad/canFam2)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of dog (May 2005 (Broad/canFam2)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both dog and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the dog assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best dog/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The dog sequence used in this annotation is from the May 2005 (Broad/canFam2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the dog/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single dog chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of "3000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetCanFam2Viewnet Net Dog (May 2005 (Broad/canFam2)), Chain and Net Alignments Comparative Genomics 
netCanFam2 Dog Net Dog (May 2005 (Broad/canFam2)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of dog (May 2005 (Broad/canFam2)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both dog and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the dog assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best dog/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The dog sequence used in this annotation is from the May 2005 (Broad/canFam2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the dog/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single dog chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of "3000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetCanFam2Viewchain Chain Dog (May 2005 (Broad/canFam2)), Chain and Net Alignments Comparative Genomics 
chainCanFam2 Dog Chain Dog (May 2005 (Broad/canFam2)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of dog (May 2005 (Broad/canFam2)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both dog and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the dog assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best dog/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The dog sequence used in this annotation is from the May 2005 (Broad/canFam2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the dog/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single dog chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of "3000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetMonDom4 Opossum Chain/Net Opossum (Jan. 2006 (Broad/monDom4)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of opossum (Jan. 2006 (Broad/monDom4)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both opossum and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the opossum assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best opossum/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The opossum sequence used in this annotation is from the Jan. 2006 (Broad/monDom4) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the opossum/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single opossum chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of "5000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetMonDom4Viewnet Net Opossum (Jan. 2006 (Broad/monDom4)), Chain and Net Alignments Comparative Genomics 
netMonDom4 Opossum Net Opossum (Jan. 2006 (Broad/monDom4)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of opossum (Jan. 2006 (Broad/monDom4)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both opossum and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the opossum assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best opossum/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The opossum sequence used in this annotation is from the Jan. 2006 (Broad/monDom4) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the opossum/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single opossum chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of "5000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetMonDom4Viewchain Chain Opossum (Jan. 2006 (Broad/monDom4)), Chain and Net Alignments Comparative Genomics 
chainMonDom4 Opossum Chain Opossum (Jan. 2006 (Broad/monDom4)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of opossum (Jan. 2006 (Broad/monDom4)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both opossum and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the opossum assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best opossum/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The opossum sequence used in this annotation is from the Jan. 2006 (Broad/monDom4) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the opossum/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single opossum chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of "5000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetOrnAna1 Platypus Chain/Net Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both platypus and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the platypus assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best platypus/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The platypus sequence used in this annotation is from the Mar. 2007 (WUGSC 5.0.1/ornAna1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the platypus/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single platypus chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of "5000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetOrnAna1Viewnet Net Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)), Chain and Net Alignments Comparative Genomics 
netOrnAna1 Platypus Net Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both platypus and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the platypus assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best platypus/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The platypus sequence used in this annotation is from the Mar. 2007 (WUGSC 5.0.1/ornAna1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the platypus/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single platypus chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of "5000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetOrnAna1Viewchain Chain Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)), Chain and Net Alignments Comparative Genomics 
chainOrnAna1 Platypus Chain Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) to the marmoset genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both platypus and marmoset simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the platypus assembly or an insertion in the marmoset assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the marmoset genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best platypus/marmoset chain for every part of the marmoset genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The platypus sequence used in this annotation is from the Mar. 2007 (WUGSC 5.0.1/ornAna1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the platypus/marmoset split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single platypus chromosome and a single marmoset chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:  ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of "5000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961