This directory contains alignments of the following assemblies:
- target/reference: Squirrel
(speTri2, Nov. 2011 (Broad/speTri2),
Broad Institute (GCA_000236235.1))
- query: Mouse
(mm39, Jun. 2020 (GRCm39/mm39),
Genome Reference Consortium Mouse Build 39 (GCA_000001635.9))
Files included in this directory:
- md5sum.txt: md5sum checksums for the files in this directory
- speTri2.mm39.all.chain.gz: chained lastz alignments. The chain format is
described in http://genome.ucsc.edu/goldenPath/help/chain.html .
- speTri2.mm39.net.gz: "net" file that describes rearrangements between
the species and the best Mouse match to any part of the
Squirrel genome. The net format is described in
http://genome.ucsc.edu/goldenPath/help/net.html .
- speTri2.mm39.net.axt.gz: chained and netted alignments,
i.e. the best chains in the Squirrel 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 .
- speTri2.mm39.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
- speTri2.mm39.syn.net.gz - filtered net file for syntenic alignments only
- reciprocalBest/ directory, contains reciprocal-best netted chains
for speTri2-mm39
The chainSwap program was used to translate mm39-referenced chained lastz
alignments to speTri2 into speTri2-referenced chains aligned to mm39. See
the download directory goldenPath/mm39/vsSpeTri2/README.txt for more
information about the mm39-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/speTri2/vsMm39/. 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 -
speTri2.mm39.net.axt.gz 2020-11-26 01:06 671M
speTri2.mm39.synNet.maf.gz 2020-11-26 01:45 629M
speTri2.mm39.all.chain.gz 2020-11-26 00:52 225M
speTri2.mm39.net.gz 2020-11-26 01:22 165M
speTri2.mm39.syn.net.gz 2020-11-26 01:31 152M
md5sum.txt 2020-11-26 01:45 291
reciprocalBest/ 2021-03-15 16:12 -