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 .