This directory contains alignments of the following assemblies:
- target/reference: Elephant
(loxAfr3, Jul. 2009 (Broad/loxAfr3),
Broad Institute loxAfr3 (NCBI project 12569, AAGU03000000))
- 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
- loxAfr3.mm39.all.chain.gz: chained lastz alignments. The chain format is
described in http://genome.ucsc.edu/goldenPath/help/chain.html .
- loxAfr3.mm39.net.gz: "net" file that describes rearrangements between
the species and the best Mouse match to any part of the
Elephant genome. The net format is described in
http://genome.ucsc.edu/goldenPath/help/net.html .
- loxAfr3.mm39.net.axt.gz: chained and netted alignments,
i.e. the best chains in the Elephant 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 .
- loxAfr3.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
- loxAfr3.mm39.syn.net.gz - filtered net file for syntenic alignments only
- reciprocalBest/ directory, contains reciprocal-best netted chains
for loxAfr3-mm39
The chainSwap program was used to translate mm39-referenced chained lastz
alignments to loxAfr3 into loxAfr3-referenced chains aligned to mm39. See
the download directory goldenPath/mm39/vsLoxAfr3/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/loxAfr3/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 -
reciprocalBest/ 2021-03-15 14:58 -
md5sum.txt 2020-11-25 04:42 291
loxAfr3.mm39.synNet.maf.gz 2020-11-25 04:42 471M
loxAfr3.mm39.syn.net.gz 2020-11-25 04:31 124M
loxAfr3.mm39.net.gz 2020-11-25 04:22 132M
loxAfr3.mm39.net.axt.gz 2020-11-25 04:08 500M
loxAfr3.mm39.all.chain.gz 2020-11-25 03:58 273M