This directory contains the Btau_2.0 cow genome assembly (bosTau2,
Mar. 2005) produced by the Baylor College of Medicine Human Genome
Sequencing Center. For more information about these data, see the
Baylor web page at http://www.hgsc.bcm.tmc.edu/projects/bovine/.
Files in this directory include:
bosTau2.2bit - contains the complete cow/bosTau2 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
bosTau2.hardmask.fa.gz
Repeats from RepeatMasker and Tandem Repeats Finder (with period
of 12 or less) are shown as Ns; non-repeating sequence is
shown in upper case.
bosTau2.softmask.fa.gz
Repeats from RepeatMasker are shown in lower case; non-repeating
sequence is shown in upper case.
bosTau2.softmask2.fa.gz
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. RepeatMasker July 2004 version with RepBase
libraries: RepBase Update 9.04, RM database version 20040702.
est.fa.gz - Cow ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
md5sum.txt - MD5 checksum of these files to verify correct transmission.
mrna.fa.gz - Cow mRNA from GenBank. This sequence data is updated once a
week via automatic GenBank updates.
UCSC_Cow2.0.agp.gz - Description of how the assembly was generated from
fragments. Downloaded from Baylor Jul. 18, 2005.
UCSC_Cow2.0.fa.gz - Sequences downloaded from Baylor Jul. 18, 2005.
UCSC modifications made to the original data set:
- Chr changed to chr
- Chr30 renamed to chrX
- ChrUn split into scaffold1 through scaffold98058
- Bin0 fragments assembled into artificial chromosome chrBin0
with 500 bp-gap padding
- chrM obtained from NCBI (gi=12800)
bosTau2.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 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/bosTau2/bigZips. To download multiple files, use
the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Please review the restrictions on the use of the cow assembly data at
http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html.
Name Last modified Size Description
Parent Directory -
est.fa.gz.md5 2019-10-16 19:38 44
mrna.fa.gz.md5 2019-10-16 19:31 45
refMrna.fa.gz.md5 2019-10-16 19:38 48
xenoRefMrna.fa.gz.md5 2019-10-16 19:38 52
upstream1000.fa.gz.md5 2019-10-16 19:39 53
upstream2000.fa.gz.md5 2019-10-16 19:40 53
upstream5000.fa.gz.md5 2019-10-16 19:41 53
md5sum.txt 2014-02-03 10:20 324
bosTau2.chrom.sizes 2005-07-23 15:45 1.7M
upstream1000.fa.gz 2019-10-16 19:39 3.0M
upstream2000.fa.gz 2019-10-16 19:40 5.7M
refMrna.fa.gz 2019-10-16 19:38 11M
mrna.fa.gz 2019-10-16 19:31 11M
upstream5000.fa.gz 2019-10-16 19:41 13M
UCSC_Cow2.0.agp.gz 2005-07-23 16:27 15M
bosTau2.fa.out.gz 2005-07-25 03:20 170M
est.fa.gz 2019-10-16 19:38 314M
xenoRefMrna.fa.gz 2019-10-16 19:38 320M
bosTau2.hardmask.fa.gz 2005-07-26 13:33 513M
UCSC_Cow2.0.fa.gz 2005-07-23 16:29 838M
bosTau2.2bit 2005-07-26 13:38 883M
bosTau2.softmask.fa.gz 2005-07-26 13:28 892M
bosTau2.softmask2.fa.gz 2005-07-26 13:30 892M
bosTau2.fa.gz 2020-01-23 02:19 892M