sangerGene WormBase Genes WormBase Gene Annotations Genes and Gene Predictions Description The WormBase Genes track shows Sanger Gene predictions from the Wormbase v. WS190 files downloaded from the Sanger Institute FTP site. This track shows the subset of data annotated as "curated", or "Coding_transcript" followed by one of these strings: "intron", "coding_exon", "exon", "cds", "three_prime_UTR", or "five_prime_UTR" in the gff files. Credits The Sanger gene predictions are produced by WormBase. Thanks to the WormBase Consortium for providing these data. 
sangerRnaGene WormBase RNAs WormBase RNA Annotations Genes and Gene Predictions Description The WormBase Genes track shows RNA predictions from the Wormbase v. WS190 files downloaded from the Sanger Institute FTP site. This track shows the subset of data annotated as "miRNA", "ncRNA", "rRNA", "scRNA", "snRNA" ,"snlRNA" ,"snoRNA" ,"tRNA", or "tRNAscan-SE-1.23" in the gff files. Credits The Sanger gene predictions are produced by WormBase. Thanks to the WormBase Consortium for providing these data. 
sangerPseudoGene WormBase PseudoGenes WormBase PseudoGene Annotations Genes and Gene Predictions Description The WormBase Genes track shows pseudogene predictions from the Wormbase v. WS190 files downloaded from the Sanger Institute FTP site. This track shows the subset of data annotated as "Pseudogene" in the gff files. Credits The Sanger gene predictions are produced by WormBase. Thanks to the WormBase Consortium for providing these data. 
refGene RefSeq Genes RefSeq Genes Genes and Gene Predictions Description The RefSeq Genes track shows known C. elegans 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. 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. This page is accessed via the small button to the left of the track's graphical display or through the link on the track's control menu. 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. Go to the Coloring Gene Predictions and Annotations by Codon page for more information about this feature. 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 C. elegans 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, 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 C. elegans ESTs That Have Been Spliced mRNA and EST Description This track shows alignments between C. elegans 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. one that is at least 32 bases in length and has 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 C. elegans 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. 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. 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, C. elegans 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, 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 
algBinding ALG-1 binding ALG-1 Argonaute binding sites Expression and Regulation Description The ALG-1 CLIP-seq tracks show the density of reads that were mapped to the C. elegans genome from independent ALG-1 CLIP-seq experiments in larval stage 4 (L4) wildtype and ALG-1 mutant worms. The regions determined to be occupied by ALG-1, as indicated by the analyses described below, are also available in the ALG-1 binding sites in larval stage 4 worms track. Genic regions were defined based on RNA-seq reads publicly available from Hillier et al., 2009. The reannotated genic regions are displayed as the subtrack "Reannotated genic regions based on data from L3 and L4 RNAseq from Hillier et al". ALG-1 is a C. elegans Argonaute protein that mediates the interaction of miRNAs and their mRNA targets. CLIP-seq is a biochemical approach to determine RNA-protein interaction loci. Methods Cross-linking immunoprecipitation, followed by deep sequencing (CLIP-seq), was performed on the Argonaute protein ALG-1 in both wild-type (WT) and ALG-1 mutant (MT) L4 worms. Reads were aligned to the C. elegans genome (ce6) using bowtie (version 0.9.9.2) from three independent CLIP-seq experiments in both WT and ALG-1 worms. Reads were computationally extended 50nt in the 3' direction to account for the expected size of PCR products that were sequenced. Biologically reproducible regions were determined based on gene-specific weighting of reads in each of the 3 experiments in the two experimental conditions (WT and MT). Reads in each of the experimental conditions were then collapsed, and biologically reproducible regions were further scrutinized for significance above background using the Poisson distribution on pre-mRNA. Regions that passed the Poisson-derived density cutoff and overlapped at least 25% of their length between WT and MT experiments were eliminated, and thus ALG-1 binding sites are defined as regions that are reproducible in independent biological experiments, contain more reads than expected by the Poisson distribution, and do not appear in MT experiments. RNA-seq reads from Hillier et al. in L3 and L4 worms were used to extend annotated genic regions into untranslated regions. Detailed descriptions of these methods can be found in the online supplementary materials for Zisoulis et al, 2010. Credits Data for this track were supplied to UCSC by the Gene Yeo lab in the Department of Cellular and Molecular Medicine, University of California, San Diego, CA. References Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH. Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res. 2009 Apr;19(4):657-66. PMID: 19181841; PMC: PMC2665784 Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo GW. Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nat Struct Mol Biol. 2010 Feb;17(2):173-9. PMID: 20062054; PMC: PMC2834287 
algBindingViewwild Wild type ALG-1 Argonaute binding sites Expression and Regulation 
wt3Forward WildT 3 F Wild type Experiment 3 forward strand Expression and Regulation 
wt3Reverse WildT 3 R Wild type Experiment 3 reverse strand Expression and Regulation 
wt2Forward WildT 2 F Wild type Experiment 2 forward strand Expression and Regulation 
wt2Reverse WildT 2 R Wild type Experiment 2 reverse strand Expression and Regulation 
wt1Forward WildT 1 F Wild type Experiment 1 forward strand Expression and Regulation 
wt1Reverse WildT 1 R Wild type Experiment 1 reverse strand Expression and Regulation 
algBindingViewsites Sites ALG-1 Argonaute binding sites Expression and Regulation 
algBindGenic Genic regions Reannotated genic regions based on data from L3 and L4 RNAseq from Hillier et al Expression and Regulation 
algBindSites Binding Sites ALG-1 binding sites in larval stage 4 worms Expression and Regulation 
algBindingViewmutant Mutant ALG-1 Argonaute binding sites Expression and Regulation 
mt3Forward Mutant 3 F Mutant Experiment 3 forward strand Expression and Regulation 
mt3Reverse Mutant 3 R Mutant Experiment 3 reverse strand Expression and Regulation 
mt2Forward Mutant 2 F Mutant Experiment 2 forward strand Expression and Regulation 
mt2Reverse Mutant 2 R Mutant Experiment 2 reverse strand Expression and Regulation 
mt1Forward Mutant 1 F Mutant Experiment 1 forward strand Expression and Regulation 
mt1Reverse Mutant 1 R Mutant Experiment 1 reverse strand Expression and Regulation 
gold Assembly Assembly from Fragments Mapping and Sequencing Description This track shows the finished assembly of the C. elegans genome. This assembly merges contigs from overlapping drafts and finished clones into longer sequence contigs. The sequence contigs are ordered and oriented when possible by mRNA, EST, paired plasmid reads (from the SNP Consortium) and BAC end sequence pairs. In the WS190 assembly, all the clones are finished and are of clone type "F". In dense mode, this track depicts the path through the finished clones (aka the golden path) used to create the assembled sequence. Clone boundaries are distinguished by the use of alternating gold and brown coloration. There are no gaps in this assembly. Credits The May 2008 Caenorhabditis elegans assembly is based on sequence version WS190 deposited into WormBase as of 28 May 2008. The sequence was produced jointly by the Sanger Institute in Hinxton, England and the Genome Sequencing Center in St. Louis. 
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 
est C. elegans ESTs C. elegans ESTs Including Unspliced mRNA and EST Description This track shows alignments between C. elegans 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. 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. 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, C. elegans 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, 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 
mrna C. elegans mRNAs C. elegans mRNAs from GenBank mRNA and EST Description The mRNA track shows alignments between C. elegans 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. 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. Methods GenBank C. elegans 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, 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 
ensGene Ensembl Genes Ensembl Genes Genes and Gene Predictions Description These gene predictions were generated by Ensembl. For more information on the different gene tracks, see our Genes FAQ. Methods For a description of the methods used in Ensembl gene predictions, please refer to Hubbard et al. (2002), also listed in the References section below. Data access Ensembl Gene data can be explored interactively using the Table Browser or the Data Integrator. For local downloads, the genePred format files for ce6 are available in our downloads directory as ensGene.txt.gz or in our genes download directory in GTF format. For programmatic access, the data can be queried from the REST API or directly from our public MySQL servers. Instructions on this method are available on our MySQL help page and on our blog. Previous versions of this track can be found on our archive download server. Credits We would like to thank Ensembl for providing these gene annotations. For more information, please see Ensembl&#39s genome annotation page. References Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T et al. The Ensembl genome database project. Nucleic Acids Res. 2002 Jan 1;30(1):38-41. PMID: 11752248; PMC: PMC99161 
gap Gap Gap Locations Mapping and Sequencing Description There are no gaps in the WS190 C. elegans assembly. Credits The May 2008 Caenorhabditis elegans assembly is based on sequence version WS190 deposited into WormBase as of 28 May 2008. The sequence was produced jointly by the Sanger Institute in Hinxton, England and the Genome Sequencing Center in St. Louis. 
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. 
nestedRepeats Interrupted Rpts Fragments of Interrupted Repeats Joined by RepeatMasker ID Variation and Repeats Description This track shows joined fragments of interrupted repeats extracted from the output of the RepeatMasker program which screens DNA sequences for interspersed repeats and low complexity DNA sequences using 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. The detailed annotations from RepeatMasker are in the RepeatMasker track. This track shows fragments of original repeat insertions which have been interrupted by insertions of younger repeats or through local rearrangements. The fragments are joined using the ID column of RepeatMasker output. Display Conventions and Configuration In pack or full mode, each interrupted repeat is displayed as boxes (fragments) joined by horizontal lines, labeled with the repeat name. If all fragments are on the same strand, arrows are added to the horizontal line to indicate the strand. In dense or squish mode, labels and arrows are omitted and in dense mode, all items are collapsed to fit on a single row. Items are shaded according to the average identity score of their fragments. Usually, the shade of an item is similar to the shades of its fragments unless some fragments are much more diverged than others. The score displayed above is the average identity score, clipped to a range of 50% - 100% and then mapped to the range 0 - 1000 for shading in the browser. Methods UCSC has used the most current versions of the RepeatMasker software and repeat libraries available to generate these data. Note that these versions may be newer than those that are publicly available on the Internet. Data are generated using the RepeatMasker -s flag. Additional flags may be used for certain organisms. 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 
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 
xenoMrna Other mRNAs Non-C. elegans mRNAs from GenBank mRNA and EST Description This track displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank from organisms other than C. elegans. 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 (+/-) for this track is in two parts. The first + indicates the orientation of the query sequence whose translated protein produced the match (here always 5' to 3', hence +). The second + or - indicates the orientation of the matching translated genomic sequence. Because the two orientations of a DNA sequence give different predicted protein sequences, there are four combinations. ++ is not the same as --, nor is +- the same as -+. 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. 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. Methods The mRNAs were aligned against the C. elegans genome using translated blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only those alignments having a base identity level within 1% of the best and at least 25% 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, 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 
xenoRefGene Other RefSeq Non-C. elegans RefSeq Genes Genes and Gene Predictions Description This track shows known protein-coding and non-protein-coding genes for organisms other than C. elegans, 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 C. elegans 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 
pubs Publications Publications: Sequences in Scientific Articles Literature Description This track is based on text-mining of full-text biomedical articles and includes two types of subtracks: Sequences found in publications, grouped by article and searched in genomes with BLAT Identifiers in publications that directly relate to chromosome locations (e.g., gene symbols, SNP identifiers, etc) Both sources of information are linked to the respective articles. Background information on how permission to full-text data was obtained can be found on the project website. Display Convention and Configuration The sequence subtrack indicates the location of sequences in publications mapped back to the genome, annotated with the first author and the year of the publication. All matches of one article are grouped ("chained") together. Article titles are shown when you move the mouse cursor over the features. Thicker parts of the features (exons) represent matching sequences, connected by thin lines to matches from the same article within 30 kbp. The subtrack "individual sequence matches" activates automatically when the user clicks a sequence match and follows the link "Show sequence matches individually" from the details page. Mouse-overs show flanking text around the sequence, and clicking features links to BLAT alignments. All other subtracks (i.e. bands, genes, SNPs) show the number of matching articles as the feature description. Clicking on them shows the sentences and sections in articles where the identifiers were found. The track configuration includes a keyword and year filter. Keywords are space-separated and are searched in the article's title, author list, and abstract. Data The track is based on text from biomedical research articles, obtained as part of the UCSC Genocoding Project. The current dataset consists of about 600,000 files (main text and supplementary files) from PubMed Central (Open-Access set) and around 6 million text files (main text) from Elsevier (as part of the Sciverse Apps program). Methods All file types (including XML, raw ASCII, PDFs and various Microsoft Office formats (Excel, Word, PowerPoint)) were converted to text. The results were processed to find groups of words that look like DNA/RNA sequences or words that look like protein sequences. These were then mapped with BLAT to the human genome and these model organisms: mouse (mm9), rat (rn4), zebrafish (danRer6), Drosophila melanogaster (dm3), X. tropicalis (xenTro2), Medaka (oryLat2), C. intestinalis (ci2), C. elegans (ce6) and yeast (sacCer2). The pipeline roughly proceeds through these steps: For sequences, the best match across all genomes is used, if it is longer than 17 bp and matches at 90% identity. Two sets of BLAT parameters are tried, the default ones for sequences longer than 25 bp, very sensitive ones (stepSize=5) for shorter sequences. Sequences are mapped to genomic DNA. Those that do not match are mapped to RefSeq cDNAs. Hits from the same article that are closer than 30 kbp are joined into one feature (shown as exon-blocks on the browser). All parts of a joined feature have to match at least 25 bp. Non-unique hits are kept in the joined feature with the most members. Joined features with identical members in two different genomes are kept in both genomes. Note that due to the 90% identity filter, some sequences do not match anywhere in the genome. Examples include primers with added restriction sites, mutation primers, or any other sequence that joins or mixes two pieces of genomic DNA not part of RefSeq. Also note that some gene symbols correspond to English words which can sometimes lead to many false positives. Credits Software and processing by Maximilian Haeussler. UCSC Track visualisation by Larry Meyer and Hiram Clawson. Elsevier support by Max Berenstein, Raphael Sidi, Judd Dunham, Scott Robbins and colleagues. Original version written at the Bergman Lab, University of Manchester, UK. Testing by Mary Mangan, OpenHelix Inc, and Greg Roe, UCSC. Feedback Please send ideas, comments or feedback on this track to max@soe.ucsc.edu. We are very interested in getting access to more articles from publishers for this dataset; see the project website. References Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM, Open Regulatory Annotation Consortium. Text-mining assisted regulatory annotation. Genome Biol. 2008;9(2):R31. PMID: 18271954; PMC: PMC2374703 Haeussler M, Gerner M, Bergman CM. Annotating genes and genomes with DNA sequences extracted from biomedical articles. Bioinformatics. 2011 Apr 1;27(7):980-6. PMID: 21325301; PMC: PMC3065681 Van Noorden R. Trouble at the text mine. Nature. 2012 Mar 7;483(7388):134-5. 
pubsBlat Sequences Sequences in Articles: PubmedCentral and Elsevier Literature 
pubsBlatPsl Indiv. Seq. Matches Individual Sequence Matches of One Selected Article from Sequences Track Literature 
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 
tRNAs tRNA Genes Transfer RNA Genes Identified with tRNAscan-SE Genes and Gene Predictions Description This track displays tRNA genes predicted by using tRNAscan-SE v.1.23. tRNAscan-SE is an integrated program that uses tRNAscan (Fichant) and an A/B box motif detection algorithm (Pavesi) as pre-filters to obtain an initial list of tRNA candidates. The program then filters these candidates with a covariance model-based search program COVE (Eddy) to obtain a highly specific set of primary sequence and secondary structure predictions that represent 99-100% of true tRNAs with a false positive rate of fewer than 1 per 15 gigabases. Detailed tRNA annotations for eukaryotes, bacteria, and archaea are available at Genomic tRNA Database (GtRNAdb). What does the tRNAscan-SE score mean? Anything with a score above 20 bits is likely to be derived from a tRNA, although this does not indicate whether the tRNA gene still encodes a functional tRNA molecule (i.e. tRNA-derived SINES probably do not function in the ribosome in translation). Vertebrate tRNAs with scores of >60.0 (bits) are likely to encode functional tRNA genes, and those with scores below ~45 have sequence or structural features that indicate they probably are no longer involved in translation. tRNAs with scores between 45-60 bits are in the "grey" zone, and may or may not have all the required features to be functional. In these cases, tRNAs should be inspected carefully for loss of specific primary or secondary structure features (usually in alignments with other genes of the same isotype), in order to make a better educated guess. These rough score range guides are not exact, nor are they based on specific biochemical studies of atypical tRNA features, so please treat them accordingly. Please note that tRNA genes marked as "Pseudo" are low scoring predictions that are mostly pseudogenes or tRNA-derived elements. These genes do not usually fold into a typical cloverleaf tRNA secondary structure and the provided images of the predicted secondary structures may appear rotated. Credits Both tRNAscan-SE and GtRNAdb are maintained by the Lowe Lab at UCSC. Cove-predicted tRNA secondary structures were rendered by NAVIEW (c) 1988 Robert E. Bruccoleri. References When making use of these data, please cite the following articles: Chan PP, Lowe TM. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 2009 Jan;37(Database issue):D93-7. PMID: 18984615; PMC: PMC2686519 Eddy SR, Durbin R. RNA sequence analysis using covariance models. Nucleic Acids Res. 1994 Jun 11;22(11):2079-88. PMID: 8029015; PMC: PMC308124 Fichant GA, Burks C. Identifying potential tRNA genes in genomic DNA sequences. J Mol Biol. 1991 Aug 5;220(3):659-71. PMID: 1870126 Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997 Mar 1;25(5):955-64. PMID: 9023104; PMC: PMC146525 Pavesi A, Conterio F, Bolchi A, Dieci G, Ottonello S. Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of transcriptional control regions. Nucleic Acids Res. 1994 Apr 11;22(7):1247-56. PMID: 8165140; PMC: PMC523650 
cons6way Conservation Multiz Alignment & Conservation (6 nematodes) Comparative Genomics Description This track shows a measure of evolutionary conservation in C. elegans, C. remanei, C. briggsae, C. brenneri, C. japonica and P. pacificus 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 typerepeats masked by C. elegans (WS190)Caenorhabditis elegans May 2008 (WS190/ce6)ce6reference species repeat masker C. remaneiCaenorhabditis remanei May 2007caeRem3chain net window masker C. briggsaeCaenorhabditis briggsae Jan 2007cb3chain net repeat masker C. brenneriCaenorhabditis brenneri Feb 2008caePb2chain net window masker C. japonicaCaenorhabditis japonica Mar 2008caeJap1chain net window masker P. pacificusPristionchus pacificus May 2007priPac1chain net window masker Table 1. Genome assemblies included in the 9-way Conservation track. Display Conventions and Configuration In full and pack display modes, conservation scores are displayed as a "wiggle" (histogram), where the height reflects the size of the score. Pairwise alignments of each species to the C. elegans genome are displayed below 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. The conservation wiggle 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. Checkboxes in the track configuration section allow excluding species from the pairwise display; however, this does not remove them from the conservation score display. To view detailed information about the alignments at a specific position, zoom in the display 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 C. elegans 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 C. elegans 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 C. elegans sequence at those alignment positions relative to the longest non-C. elegans sequence. If there is sufficient space in the display, the size of the gap is shown; if not, and if the gap size is a multiple of 3, a "*" is displayed, otherwise "+" is shown. 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: Gene TrackSpecies Worm Base Genes (Sanger Genes)C. elegans C. elegans mapped GenesC. remanei C. elegans mapped GenesC. briggsae C. elegans mapped GenesC. brenneri C. elegans mapped GenesC. japonica C. elegans mapped GenesP. pacificus Methods Pairwise alignments with the C. elegans genome were generated for each species using blastz from repeat-masked or window-masker 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. 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 6-way conserved tree model and 6-way non-conserved tree model for this track was constructed from the information in Kiontke et. al. (2005) with the branch length for P. pacificus arbitrarily set manually for the phastCons starting-tree model. The branch lengths in the conserved and non-conserved tree models were produced by the phastCons tuning steps using phyloBoot. The phastCons parameters used for the conservation measurement were: expected-length=15 and target-coverage=0.55 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. Note that, unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size, so 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 at UCSC 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 Kiontke and Fitch (2005). References Phylo-HMM: 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, 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 Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351. 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.c 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: Kiontke K, Fitch DH. The phylogenetic relationships of Caenorhabditis and other rhabditids. WormBook. 2005 Aug 11:1-11. PMID: 18050394 
cons6wayViewalign Multiz Alignments Multiz Alignment & Conservation (6 nematodes) Comparative Genomics 
multiz6way Multiz Align Multiz Alignments of 6 Nematodes Comparative Genomics Description This track shows a measure of evolutionary conservation in C. elegans, C. remanei, C. briggsae, C. brenneri, C. japonica and P. pacificus 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 typerepeats masked by C. elegans (WS190)Caenorhabditis elegans May 2008 (WS190/ce6)ce6reference species repeat masker C. remaneiCaenorhabditis remanei May 2007caeRem3chain net window masker C. briggsaeCaenorhabditis briggsae Jan 2007cb3chain net repeat masker C. brenneriCaenorhabditis brenneri Feb 2008caePb2chain net window masker C. japonicaCaenorhabditis japonica Mar 2008caeJap1chain net window masker P. pacificusPristionchus pacificus May 2007priPac1chain net window masker Table 1. Genome assemblies included in the 9-way Conservation track. Display Conventions and Configuration In full and pack display modes, conservation scores are displayed as a "wiggle" (histogram), where the height reflects the size of the score. Pairwise alignments of each species to the C. elegans genome are displayed below 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. The conservation wiggle 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. Checkboxes in the track configuration section allow excluding species from the pairwise display; however, this does not remove them from the conservation score display. To view detailed information about the alignments at a specific position, zoom in the display 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 C. elegans 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 C. elegans 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 C. elegans sequence at those alignment positions relative to the longest non-C. elegans sequence. If there is sufficient space in the display, the size of the gap is shown; if not, and if the gap size is a multiple of 3, a "*" is displayed, otherwise "+" is shown. 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: Gene TrackSpecies Worm Base Genes (Sanger Genes)C. elegans C. elegans mapped GenesC. remanei C. elegans mapped GenesC. briggsae C. elegans mapped GenesC. brenneri C. elegans mapped GenesC. japonica C. elegans mapped GenesP. pacificus Methods Pairwise alignments with the C. elegans genome were generated for each species using blastz from repeat-masked or window-masker 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. 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 6-way conserved tree model and 6-way non-conserved tree model for this track was constructed from the information in Kiontke et. al. (2005) with the branch length for P. pacificus arbitrarily set manually for the phastCons starting-tree model. The branch lengths in the conserved and non-conserved tree models were produced by the phastCons tuning steps using phyloBoot. The phastCons parameters used for the conservation measurement were: expected-length=15 and target-coverage=0.55 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. Note that, unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size, so 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 at UCSC 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 Kiontke and Fitch (2005). References Phylo-HMM: 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, 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 Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351. 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.c 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: Kiontke K, Fitch DH. The phylogenetic relationships of Caenorhabditis and other rhabditids. WormBook. 2005 Aug 11:1-11. PMID: 18050394 
cons6wayViewphastcons Element Conservation (phastCons) Multiz Alignment & Conservation (6 nematodes) Comparative Genomics 
phastCons6way 6 Nematode Cons 6 nematode conservation by PhastCons Comparative Genomics 
cons6wayViewelements Conserved Elements Multiz Alignment & Conservation (6 nematodes) Comparative Genomics 
phastConsElements6way 6 nematode El 6 nematode 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. 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 A, 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 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 R, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. iGenome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
nucleosome Nucleosome Nucleosome predictions from SOLiD Core Alignments Mapping and Sequencing Description Mononucleosome control track The control data was produced from the lightly micrococcal nuclease-digested paired-end sequenced genomic DNA fragments in the size range of 400-900 base pairs. Each feature corresponds to one end of the paired-end fragment with thick portion representing the sequenced 25 base pairs of that end. Features span 147 base pairs (displayed equivalently to mononucleosome data). Mononucleosome sense strand reads Mononucleosomal fragments were obtained by micrococcal nuclease digestion of C. elegans lysates, DNA extraction, and sequencing of nucleosome-bound DNA fragments. Features represent inferred 147 base pair cores from fragments that mapped to the sense strand of the reference genome. The thick portion of each feature (50 base pairs) represents the sequenced part of the nucleosome-bound fragment. Mononucleosome antisense strand reads Mononucleosomal fragments were obtained by micrococcal nuclease digestion of C. elegans lysates, DNA extraction and sequencing of nucleosome-bound DNA fragments. Features represent inferred 147 base pair cores from fragments that mapped to the antisense strands. The thick portion of each feature (50 base pairs) represents the sequenced part of the core. Display Conventions and Configuration In each of the sub-tracks, sequences starting at the same base pair were collapsed and color-coded from the lightest to the darkest color in five shades according to the following category-based scale: Number of read instancesColor shade 1lightest 2light 3-5medium 6-10dark more than 10darkest Hold your mouse over individual items in each track to see the number of read instances starting at that base pair. Credits The data for this track is supplied by the Sidow Lab and the Fire Lab at the Stanford School of Medicine. Track display advice provided by Hiram Clawson, UCSC Genome Browser Engineering. References Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 2008 Jul;18(7):1051-63. PMID: 18477713; PMC: PMC2493394 Supported oligo ligation detection (SOLiD) sequencing technology from Applied Biosystems. 
nucleosomeFragmentsAntisense fragments - mononucleosomal fragments, antisense strand reads Mapping and Sequencing 
nucleosomeFragmentsSense fragments + mononucleosomal fragments, sense strand reads Mapping and Sequencing 
nucleosomeControl Control mononucleosome control Mapping and Sequencing 
nucleosomeControlCoverage MNase Coverage Micrococcal nuclease control coverage Mapping and Sequencing Description Micrococcal nuclease control coverage, sense strand reads The plot represents local coverage by control micrococcal nuclease fragments from cleavage of naked C. elegans DNA. By analogy with the experimental nucleosome data, 147 base pair sense segments starting from each of the individual control reads has been used to assemble a control coverage plot that accounts for enzymatic and sequencing biases of sampling from the reference genome. Micrococcal nuclease control coverage, antisense strand reads The plot represents local coverage by control micrococcal nuclease fragments from cleavage of naked C. elegans DNA. By analogy with the experimental nucleosome data, 147 base pair antisense segments starting from each of the individual control reads has been used to assemble a control coverage plot that accounts for enzymatic and sequencing biases of sampling from the reference genome. Credits The data for this track is supplied by the Sidow Lab and the Fire Lab at the Stanford School of Medicine. Track display advice provided by Hiram Clawson, UCSC Genome Browser Engineering. References Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 2008 Jul;18(7):1051-63. PMID: 18477713; PMC: PMC2493394 Supported oligo ligation detection (SOLiD) sequencing technology from Applied Biosystems. 
nucleosomeControlAntisenseCoverage Cntl MNase -Covg Micrococcal nuclease control coverage, antisense strand reads Mapping and Sequencing 
nucleosomeControlSenseCoverage Cntl MNase +Covg Micrococcal nuclease control coverage, sense strand reads Mapping and Sequencing 
chainPriPac1 P. pacificus Chain P. pacificus (Feb. 2007 (WUGSC 5.0/priPac1)) Chained Alignments Comparative Genomics Description This track shows alignments of P. pacificus (priPac1, Feb. 2007 (WUGSC 5.0/priPac1)) to the C. elegans genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both P. pacificus and C. elegans 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 P. pacificus assembly or an insertion in the C. elegans 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 C. elegans 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. Display Conventions and Configuration 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. Methods Transposons that have been inserted since the P. pacificus/C. elegans split were removed from the assemblies. The abbreviated genomes were aligned with blastz using dynamic masking, and the transposons were then added back in. The resulting alignments were converted into psl format using the lavToPsl program. The axt alignments were fed into axtChain, which organizes all alignments between a single P. pacificus chromosome and a single C. elegans 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 threshold of 2000 were discarded; the remaining chains are displayed in this track. Credits Blastz was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Repeat areas we marked in the genome with WindowMasker as developed by: Morgulis A, Gertz EM, Schäffer AA, Agarwala R. 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 were generated by Robert Baertsch and Jim Kent. References 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 Morgulis A, Gertz EM, Schäffer AA, Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006 Jan 15;22(2):134-41. PMID: 16287941 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
nucleosomeDensity NSome Coverage Coverage of nucleosome predictions from SOLiD Core Alignments Mapping and Sequencing Description Coverage of mononucleosomal fragments, sense strand reads The plot represents the coverage by putative mononucleosomal cores (147 base pairs) from micrococcal nuclease cleavage of C. elegans chromatin, using reads that mapped on the sense strand of the reference genome. Coverage of mononucleosomal fragments, antisense strand reads The plot represents the coverage by putative mononucleosomal cores (147 base pairs) from micrococcal nuclease cleavage of C. elegans chromatin using reads that mapped on the antisense strand of the reference genome. Credits The data for this track is supplied by the Sidow Lab and the Fire Lab at the Stanford School of Medicine. Track display advice provided by Hiram Clawson, UCSC Genome Browser Engineering. References Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 2008 Jul;18(7):1051-63. PMID: 18477713; PMC: PMC2493394 Supported oligo ligation detection (SOLiD) sequencing technology from Applied Biosystems. 
monoNucleosomesAntiSense NSome Core -Covg Coverage of mononucleosomal fragments, antisense strand reads Mapping and Sequencing 
monoNucleosomesSense NSome Core +Covg Coverage of mononucleosomal fragments, sense strand reads Mapping and Sequencing 
netPriPac1 P. pacificus Net P. pacificus (Feb. 2007 (WUGSC 5.0/priPac1)) Alignment Net Comparative Genomics Description This track shows the best P. pacificus/C. elegans chain for every part of the C. elegans genome. It is useful for finding orthologous regions and for studying genome rearrangement. The P. pacificus sequence used in this annotation is from the Feb. 2007 (WUGSC 5.0/priPac1) (priPac1) assembly. Display Conventions and Configuration 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 Chains were derived from blastz 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 The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. Blastz was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. The browser display and database storage of the nets were made by Robert Baertsch and Jim Kent. References 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 R, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
nucleosomeAdjustedCoverage Adj NSome Covrg Adjusted nucleosome coverage (25bp) Mapping and Sequencing Methods The plot represents relative mononucleosome enrichment at each position in the genome (on a log of 2 scale). The coverage metric is given according to a formula [ (1+n)/N ] / [ (1+c)/C ] where n and c are the numbers of putative 147 base pair cores covering each base pair from nucleosome and control data, N and C are the total number of nucleosome and control reads obtained by SOLiD sequencing with 25 base pairs mapped to the reference genome. Data download The source data for this track can be fetched from our ftp server (nucleosomeAdjustedCoverage.wigAscii.gz; 450 Mb compressed, 1.6 Gb uncompressed). This data is formatted into the two-column variableStep wiggle format. Credits The data for this track is supplied by the Sidow Lab and the Fire Lab at the Stanford School of Medicine. Track display advice provided by Hiram Clawson, UCSC Genome Browser Engineering. References Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 2008 Jul;18(7):1051-63. PMID: 18477713; PMC: PMC2493394 Supported oligo ligation detection (SOLiD) sequencing technology from Applied Biosystems. 
chainCaeJap1 C. japonica Chain C. japonica (Mar. 2008 (WUGSC 3.0.2/caeJap1)) Chained Alignments Comparative Genomics Description This track shows alignments of C. japonica (caeJap1, Mar. 2008 (WUGSC 3.0.2/caeJap1)) to the C. elegans genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both C. japonica and C. elegans 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 C. japonica assembly or an insertion in the C. elegans 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 C. elegans 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. Display Conventions and Configuration 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. Methods Transposons that have been inserted since the C. japonica/C. elegans split were removed from the assemblies. The abbreviated genomes were aligned with blastz using dynamic masking, and the transposons were then added back in. The resulting alignments were converted into psl format using the lavToPsl program. The axt alignments were fed into axtChain, which organizes all alignments between a single C. japonica chromosome and a single C. elegans 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 threshold of 2000 were discarded; the remaining chains are displayed in this track. Credits Blastz was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Repeat areas we marked in the genome with WindowMasker as developed by: Morgulis A, Gertz EM, Schäffer AA, Agarwala R. 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 were generated by Robert Baertsch and Jim Kent. References 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 Morgulis A, Gertz EM, Schäffer AA, Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006 Jan 15;22(2):134-41. PMID: 16287941 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 
netCaeJap1 C. japonica Net C. japonica (Mar. 2008 (WUGSC 3.0.2/caeJap1)) Alignment Net Comparative Genomics Description This track shows the best C. japonica/C. elegans chain for every part of the C. elegans genome. It is useful for finding orthologous regions and for studying genome rearrangement. The C. japonica sequence used in this annotation is from the Mar. 2008 (WUGSC 3.0.2/caeJap1) (caeJap1) assembly. Display Conventions and Configuration 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 Chains were derived from blastz 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 The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. Blastz was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. The browser display and database storage of the nets were made by Robert Baertsch and Jim Kent. References 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 R, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
nucleosomeStringency NSome Stringency Nucleosome Positioning Stringency from SOLiD Core Alignments Mapping and Sequencing Methods The plot represents stringency of nucleosome positioning (at the dyad) as a fraction of positioned nucleosomes. Stringency metric is given by a ratio of putative mononucleosome dyad instances falling in a 23 base pair window of a given site to the number of infringing nucleosome dyads in a 300 base pair window. Credits The data for this track is supplied by the Sidow Lab and the Fire Lab at the Stanford School of Medicine. Track display advice provided by Hiram Clawson, UCSC Genome Browser Engineering. References Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 2008 Jul;18(7):1051-63. PMID: 18477713; PMC: PMC2493394 Supported oligo ligation detection (SOLiD) sequencing technology from Applied Biosystems. 
chainCaePb2 C. brenneri Chain C. brenneri (Feb. 2008 (WUGSC 6.0.1/caePb2)) Chained Alignments Comparative Genomics Description This track shows alignments of C. brenneri (caePb2, Feb. 2008 (WUGSC 6.0.1/caePb2)) to the C. elegans genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both C. brenneri and C. elegans 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 C. brenneri assembly or an insertion in the C. elegans 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 C. elegans 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. Display Conventions and Configuration 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. Methods Transposons that have been inserted since the C. brenneri/C. elegans split were removed from the assemblies. The abbreviated genomes were aligned with blastz using dynamic masking, and the transposons were then added back in. The resulting alignments were converted into psl format using the lavToPsl program. The axt alignments were fed into axtChain, which organizes all alignments between a single C. brenneri chromosome and a single C. elegans 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 threshold of 2000 were discarded; the remaining chains are displayed in this track. Credits Blastz was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Repeat areas we marked in the genome with WindowMasker as developed by: Morgulis A, Gertz EM, Schäffer AA, Agarwala R. 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 were generated by Robert Baertsch and Jim Kent. References Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrich, 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 Morgulis A, Gertz EM, Schäffer AA, Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006 Jan 15;22(2):134-41. PMID: 16287941 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
netCaePb2 C. brenneri Net C. brenneri (Feb. 2008 (WUGSC 6.0.1/caePb2)) Alignment Net Comparative Genomics Description This track shows the best C. brenneri/C. elegans chain for every part of the C. elegans genome. It is useful for finding orthologous regions and for studying genome rearrangement. The C. brenneri sequence used in this annotation is from the Feb. 2008 (WUGSC 6.0.1/caePb2) (caePb2) assembly. Display Conventions and Configuration 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 Chains were derived from blastz 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 The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. Blastz was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. The browser display and database storage of the nets were made by Robert Baertsch and Jim Kent. References 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 R, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainCb3 C. briggsae Chain C. briggsae (Jan. 2007 (WUGSC 1.0/cb3)) Chained Alignments Comparative Genomics Description This track shows alignments of C. briggsae (cb3, Jan. 2007 (WUGSC 1.0/cb3)) to the C. elegans genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both C. briggsae and C. elegans 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 C. briggsae assembly or an insertion in the C. elegans 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 C. elegans 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. Display Conventions and Configuration 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. Methods Transposons that have been inserted since the C. briggsae/C. elegans split were removed from the assemblies. The abbreviated genomes were aligned with blastz using dynamic masking, and the transposons were then added back in. The resulting alignments were converted into psl format using the lavToPsl program. The axt alignments were fed into axtChain, which organizes all alignments between a single C. briggsae chromosome and a single C. elegans 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 threshold of 2000 were discarded; the remaining chains are displayed in this track. Credits Blastz was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Repeat areas we marked in the genome with WindowMasker as developed by: Morgulis A, Gertz EM, Schäffer AA, Agarwala R. 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 were generated by Robert Baertsch and Jim Kent. References 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 Morgulis A, Gertz EM, Schäffer AA, Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006 Jan 15;22(2):134-41. PMID: 16287941 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
netCb3 C. briggsae Net C. briggsae (Jan. 2007 (WUGSC 1.0/cb3)) Alignment Net Comparative Genomics Description This track shows the best C. briggsae/C. elegans chain for every part of the C. elegans genome. It is useful for finding orthologous regions and for studying genome rearrangement. The C. briggsae sequence used in this annotation is from the Jan. 2007 (WUGSC 1.0/cb3) (cb3) assembly. Display Conventions and Configuration 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 Chains were derived from blastz 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 The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. Blastz was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. The browser display and database storage of the nets were made by Robert Baertsch and Jim Kent. References 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 R, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainCaeRem3 C. remanei Chain C. remanei (May 2007 (WUGSC 15.0.1/caeRem3)) Chained Alignments Comparative Genomics Description This track shows alignments of C. remanei (caeRem3, May 2007 (WUGSC 15.0.1/caeRem3)) to the C. elegans genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both C. remanei and C. elegans 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 C. remanei assembly or an insertion in the C. elegans 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 C. elegans 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. Display Conventions and Configuration 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. Methods Transposons that have been inserted since the C. remanei/C. elegans split were removed from the assemblies. The abbreviated genomes were aligned with blastz using dynamic masking, and the transposons were then added back in. The resulting alignments were converted into psl format using the lavToPsl program. The axt alignments were fed into axtChain, which organizes all alignments between a single C. remanei chromosome and a single C. elegans 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 threshold of 2000 were discarded; the remaining chains are displayed in this track. Credits Blastz was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Repeat areas we marked in the genome with WindowMasker as developed by: Morgulis A, Gertz EM, Schäffer AA, Agarwala R. 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 were generated by Robert Baertsch and Jim Kent. References 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 Morgulis A, Gertz EM, Schäffer AA, Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006 Jan 15;22(2):134-41. PMID: 16287941 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
netCaeRem3 C. remanei Net C. remanei (May 2007 (WUGSC 15.0.1/caeRem3)) Alignment Net Comparative Genomics Description This track shows the best C. remanei/C. elegans chain for every part of the C. elegans genome. It is useful for finding orthologous regions and for studying genome rearrangement. The C. remanei sequence used in this annotation is from the May 2007 (WUGSC 15.0.1/caeRem3) (caeRem3) assembly. Display Conventions and Configuration 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 Chains were derived from blastz 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 The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. Blastz was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. The browser display and database storage of the nets were made by Robert Baertsch and Jim Kent. References 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 R, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
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, J. (2000) in the References section below. 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) 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. Methods UCSC has used the most current versions of the RepeatMasker software and repeat libraries available to generate these data. Note that these versions may be newer than those that are publicly available on the Internet. 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 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. 
25mersRepeats 25mers 25mers repeat annotation Variation and Repeats Description Marking the repetetive 25mers in WS170. The centers of repeated 25mers are marked black and areas that are covered by the 25mers are in grey. Methods A sliding window of 25 bases was passed over the genome. Each base in the genome is the start of a 25 bp window. The number of occurrences of each of the 25mers is tabulated. Any 25mer that occurs more than once is colored grey over its 25 bp extent, and the center base is marked in black. Thus, runs of consecutive black bases indicate overlapping 25mers with their centers adjacent. Credits The data for this track is supplied by the Sidow Lab, and the Fire Lab at the Stanford School of Medicine. Track display advice provided by Hiram Clawson, UCSC Genome Browser Engineering. 
chainSelf Self Chain C. elegans Chained Self Alignments Variation and Repeats Description This track shows alignments of the C. elegans genome with itself, using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. The system can also tolerate gaps in both sets of sequence simultaneously. After filtering out the "trivial" alignments produced when identical locations of the genome map to one another (e.g. chrN mapping to chrN), the remaining alignments point out areas of duplication within the C. elegans genome. 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 query assembly or an insertion in the target assembly. Double lines represent more complex gaps that involve substantial sequence in both the query and target assemblies. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one of the assemblies. In cases where multiple chains align over a particular region of the C. elegans 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. Display Conventions and Configuration 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. Methods The genome was aligned to itself using blastz. Trivial alignments were filtered out, and the remaining alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single target chromosome and a single query 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. Chains scoring below a threshold were discarded; the remaining chains are displayed in this track. Credits 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 were generated by Robert Baertsch and Jim Kent. References 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 R, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961