This directory contains the Oct. 2007 assembly of the cow genome
(bosTau4, Baylor Release 4.0), as well as repeat annotations and GenBank sequences.
This assembly was produced by the Baylor College of Medicine Human Genome Sequencing Center.
For more information on the cow genome, see the Baylor College of Medicine
Human Genome Sequencing Center project website at
http://www.hgsc.bcm.tmc.edu/projects/bovine/
Files included in this directory:
bosTau4.2bit - contains the complete cow/bosTau4 genome sequence
in the 2bit file format. Repeats from RepeatMasker and Tandem Repeats
Finder (with period of 12 or less) are shown in lower case; non-repeating
sequence is shown in upper case. The utility program, twoBitToFa (available
from the kent src tree), can be used to extract .fa file(s) from
this file. A pre-compiled version of the command line tool can be
found at:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
See also:
http://genome.ucsc.edu/admin/git.html
http://genome.ucsc.edu/admin/jk-install.html
bosTau4.agp.gz - Description of how the assembly was generated from
fragments.
bosTau4.fa.gz - "Soft-masked" assembly sequence in one file.
Repeats from RepeatMasker and Tandem Repeats Finder (with period
of 12 or less) are shown in lower case; non-repeating sequence is
shown in upper case.
bosTau4.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
bosTau4.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting.
# Jan 11 2008 (open-3-1-9) version of RepeatMasker
# CC RELEASE 20071204;
bosTau4.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format.
est.fa.gz - Cow ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
bosTau4.quals.fa.gz - quality scores in fasta file format
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Cow mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
This sequence data is updated once a week via automatic GenBank
updates.
upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription starts for MGC Genes with annotated 5' UTRs.
This file is updated weekly so it could be slightly out
of synch with the MGC Gene data which is updated daily for most
assemblies.
upstream2000.fa.gz - Same as upstream1000, but 2000 bases.
upstream5000.fa.gz - Same as upstream1000, but 5000 bases.
xenoMrna.fa.gz - GenBank mRNAs from species other than that of
the genome. This sequence data is updated once a week via automatic
GenBank updates.
bosTau4.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
------------------------------------------------------------------
If you plan to download a large file or multiple files from this
directory, we recommend that you use ftp rather than downloading the
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/bosTau4/bigZips. To download multiple files, use
the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Alternate methods to ftp access.
Using an rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/bigZips/chromFa.tar.gz'
-O chromFa.tar.gz
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
For conditions of use regarding the Cow genome sequence data, see
http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html .
Name Last modified Size Description
Parent Directory -
bosTau4.2bit 2008-03-10 11:27 729M
bosTau4.agp.gz 2008-03-19 15:38 2.9M
bosTau4.chrom.sizes 2008-03-07 15:55 238K
bosTau4.fa.gz 2008-03-19 15:53 857M
bosTau4.fa.masked.gz 2008-03-19 16:02 483M
bosTau4.fa.out.gz 2008-03-19 15:39 161M
bosTau4.quals.fa.gz 2009-06-09 10:30 354M
bosTau4.trf.bed.gz 2008-03-19 15:40 2.6M
est.fa.gz 2019-10-16 19:12 314M
est.fa.gz.md5 2019-10-16 19:12 44
genes/ 2020-02-05 13:46 -
md5sum.txt 2014-01-03 14:54 358
mrna.fa.gz 2019-10-16 19:06 11M
mrna.fa.gz.md5 2019-10-16 19:06 45
refMrna.fa.gz 2019-10-16 19:13 11M
refMrna.fa.gz.md5 2019-10-16 19:13 48
upstream1000.fa.gz 2019-10-16 19:13 2.8M
upstream1000.fa.gz.md5 2019-10-16 19:13 53
upstream2000.fa.gz 2019-10-16 19:13 5.3M
upstream2000.fa.gz.md5 2019-10-16 19:13 53
upstream5000.fa.gz 2019-10-16 19:14 13M
upstream5000.fa.gz.md5 2019-10-16 19:14 53
xenoMrna.fa.gz 2016-03-22 13:14 5.0G
xenoMrna.fa.gz.md5 2016-03-22 13:14 49
xenoRefMrna.fa.gz 2019-10-16 19:12 320M
xenoRefMrna.fa.gz.md5 2019-10-16 19:13 52