This directory contains the August 2006 assembly of the cow genome
(bosTau3, Baylor Btau_3.1).  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/projects/bovine/ .

Files included in this directory:

chr*.fa.gz: gzip compressed FASTA sequence of each chromosome.
    Repeats (from RepeatMasker and Tandem Repeat Finder) 
    are in lower case while non-repeating sequence is in upper case.
    RepeatMasker version: October 6 2006 (open-3-1-6)
    libraries: RepBase Update, RM database version 20061006

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

UCSC modifications made to the original data set:
 - Chr changed to chr
 - Chr30 renamed to chrX
 - ChrUn kept in separate scaffolds

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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/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.