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:

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:
    See also:

bosTau3.agp.gz - Description of how the assembly was generated from

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

md5sum.txt - checksums of files in this directory

bosTau3.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, 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 .

      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