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) 

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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.