This directory contains the October 2006 assembly of the cow genome
(bosTau4, Baylor Release 4.0).  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:
<A HREF="http://www.hgsc.bcm.tmc.edu/projects/bovine/"
TARGET=_blank>Baylor College of Medicine Human Genome Sequencing Center</A>

Files included in this directory:

chr*.fa.gz: gzip compressed FASTA sequence of each chromosome.
    Repeats (from RepeatMasker (-s) and Tandem Repeat Finder) 
    are in lower case while non-repeating sequence is in upper case.
    RepeatMasker version: Jan 11 2008 (open-3-1-9)
    libraries:  CC   RELEASE 20071204;

chrUn.scaffolds.fa.gz: components of Baylor ChrUn artificial chromosome
    treated as separate scaffolds. Treatment is otherwise the same
    as for chr*.fa.gz above.

md5sum.txt - MD5 checksum of these files to verify correct transmission

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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/bosTau4/chromosomes. To download 
multiple files, use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory)


To unpack the fa.gz files:
    gunzip <file>.fa.gz

Please review the restrictions on the use of the cow assembly data at
http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html.