This directory contains alignments of the following assemblies:
- target/reference: African clawed frog
(xenLae2, Aug. 2016 (Xenopus_laevis_v2/xenLae2),
International Xenopus Sequencing Consortium)
- query: X. tropicalis
(xenTro9, Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9),
DOE Joint Genome Institute)
Files included in this directory:
- md5sum.txt: md5sum checksums for the files in this directory
- xenLae2.xenTro9.all.chain.gz: chained blastz alignments. The chain format is
described in http://genome.ucsc.edu/goldenPath/help/chain.html .
- xenLae2.xenTro9.net.gz: "net" file that describes rearrangements between
the species and the best X. tropicalis match to any part of the
African clawed frog genome. The net format is described in
http://genome.ucsc.edu/goldenPath/help/net.html .
- xenLae2.xenTro9.net.axt.gz: chained and netted alignments,
i.e. the best chains in the African clawed frog genome, with gaps in the best
chains filled in by next-best chains where possible. The axt format is
described in http://genome.ucsc.edu/goldenPath/help/axt.html .
- xenLae2.xenTro9.synNet.maf.gz - filtered net file for syntenic alignments
only, in MAF format, see also, description of MAF format:
http://genome.ucsc.edu/FAQ/FAQformat.html#format5
- xenLae2.xenTro9.syn.net.gz - filtered net file for syntenic alignments only
- reciprocalBest/ directory, contains reciprocal-best netted chains
for xenLae2-xenTro9
The chainSwap program was used to translate xenTro9-referenced chained blastz
alignments to xenLae2 into xenLae2-referenced chains aligned to xenTro9. See
the download directory goldenPath/xenTro9/vsXenLae2/README.txt for more
information about the xenTro9-referenced blastz and chaining process.
Chained alignments were processed into nets by the chainNet, netSyntenic,
and netClass programs.
Best-chain alignments in axt format were extracted by the netToAxt program.
All programs run after blastz were written by Jim Kent at UCSC.
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If you plan to download a large file or multiple files from this directory,
we recommend you use ftp rather than downloading the files via our website.
To do so, ftp to hgdownload.cse.ucsc.edu, then go to the directory
goldenPath/xenLae2/vsXenTro9/. To download multiple files, use the "mget"
command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all files in the current directory)
All files in this directory are freely available for public use.
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References
Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence
alignments. Pac Symp Biocomput. 2002:115-26.
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.
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.
Name Last modified Size Description
Parent Directory -
reciprocalBest/ 2017-04-12 01:54 -
md5sum.txt 2017-04-07 22:08 306
xenLae2.xenTro9.synNet.maf.gz 2017-04-07 22:08 566M
xenLae2.xenTro9.syn.net.gz 2017-04-07 21:46 108M
xenLae2.xenTro9.net.gz 2017-04-07 19:55 179M
xenLae2.xenTro9.net.axt.gz 2017-04-07 14:30 810M
xenLae2.xenTro9.all.chain.gz 2017-04-06 13:58 2.7G