This directory contains alignments of the following assemblies:
- target/reference: Medaka
(oryLat2, Oct. 2005 (NIG/UT MEDAKA1/oryLat2),
NIG and Tokyo Univ MEDAKA1 (NCBI project 16702, BAAF04000000))
- query: Chicken
(galGal6, Mar. 2018 (GRCg6a/galGal6),
Genome Reference Consortium)
Files included in this directory:
- md5sum.txt: md5sum checksums for the files in this directory
- oryLat2.galGal6.all.chain.gz: chained lastz alignments. The chain format is
described in http://genome.ucsc.edu/goldenPath/help/chain.html .
- oryLat2.galGal6.net.gz: "net" file that describes rearrangements between
the species and the best Chicken match to any part of the
Medaka genome. The net format is described in
http://genome.ucsc.edu/goldenPath/help/net.html .
- oryLat2.galGal6.net.axt.gz: chained and netted alignments,
i.e. the best chains in the Medaka 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 .
- oryLat2.galGal6.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
- oryLat2.galGal6.syn.net.gz - filtered net file for syntenic alignments only
- reciprocalBest/ directory, contains reciprocal-best netted chains
for oryLat2-galGal6
The chainSwap program was used to translate galGal6-referenced chained lastz
alignments to oryLat2 into oryLat2-referenced chains aligned to galGal6. See
the download directory goldenPath/galGal6/vsOryLat2/README.txt for more
information about the galGal6-referenced lastz 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 lastz 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.soe.ucsc.edu, then go to the directory
goldenPath/oryLat2/vsGalGal6/. 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
Harris, R.S. (2007) Improved pairwise alignment of genomic DNA
Ph.D. Thesis, The Pennsylvania State University
Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence
alignments. Pac Symp Biocomput. 2002:115-26.
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 -
oryLat2.galGal6.net.axt.gz 2018-10-26 07:25 40M
oryLat2.galGal6.all.chain.gz 2018-10-26 07:23 18M
oryLat2.galGal6.synNet.maf.gz 2018-10-26 07:28 11M
oryLat2.galGal6.net.gz 2018-10-26 07:26 9.0M
oryLat2.galGal6.syn.net.gz 2018-10-26 07:27 2.0M
md5sum.txt 2018-10-26 07:28 306
reciprocalBest/ 2018-10-26 08:56 -