This directory contains the August 2006 assembly of the cow genome
(bosTau3, Baylor Release 3.1), 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 project website: http://www.hgsc.bcm.tmc.edu/.
Files included in this directory:
bosTau3.2bit - contains the complete cow/bosTau3 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
bosTau3.agp.gz - Description of how the assembly was generated from
fragments.
bosTau3.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.
bosTau3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
bosTau3.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting.
RepeatMasker version: October 6 2006 (open-3-1-6)
RepBase Update / RepeatMasker library version: 20061006
bosTau3.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.
md5sum.txt - checksums of files in this directory
bosTau3.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
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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, then
go to the directory goldenPath/bosTau3/bigZips. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
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 -
bosTau3.2bit 2007-02-23 16:58 726M
bosTau3.agp.gz 2007-03-19 10:43 2.8M
bosTau3.chrom.sizes 2006-10-02 10:55 264K
bosTau3.fa.gz 2007-03-19 10:58 858M
bosTau3.fa.masked.gz 2007-03-19 11:07 487M
bosTau3.fa.out.gz 2007-03-19 10:44 162M
bosTau3.trf.bed.gz 2007-03-19 10:44 2.4M
est.fa.gz 2019-10-16 19:27 314M
est.fa.gz.md5 2019-10-16 19:27 44
genes/ 2020-02-05 13:46 -
md5sum.txt 2014-01-27 15:49 304
mrna.fa.gz 2019-10-16 19:20 11M
mrna.fa.gz.md5 2019-10-16 19:20 45
refMrna.fa.gz 2019-10-16 19:27 11M
refMrna.fa.gz.md5 2019-10-16 19:27 48
upstream1000.fa.gz 2019-10-16 19:28 3.4M
upstream1000.fa.gz.md5 2019-10-16 19:28 53
upstream2000.fa.gz 2019-10-16 19:28 6.5M
upstream2000.fa.gz.md5 2019-10-16 19:28 53
upstream5000.fa.gz 2019-10-16 19:29 16M
upstream5000.fa.gz.md5 2019-10-16 19:29 53
xenoMrna.fa.gz 2016-03-22 15:07 5.0G
xenoMrna.fa.gz.md5 2016-03-22 15:07 49
xenoRefMrna.fa.gz 2019-10-16 19:27 320M
xenoRefMrna.fa.gz.md5 2019-10-16 19:27 52