This directory contains alignments of the cow assembly 
(bosTau1, Sept. 2004) to the human assembly (hg17, May 2004).

Files included in this directory:

  - axtNet directory: contains chained and netted alignments, i.e. the
    best chains in the genome, with gaps in the best chains filled in 
    by next-best chains where possible. 

  - cow.chain.gz: chained blastz alignments. The chain format is 
    described in http://genome.ucsc.edu/goldenPath/help/chain.html.

  - cow.net.gz: "net" file that describes rearrangements between 
    the species and the best cow match to any part of the human 
    genome.  The net format is described in 
    http://genome.ucsc.edu/goldenPath/help/net.html.

The alignments in the axtNet directory are in "axt" format.  For a
description, see http://genome.ucsc.edu/goldenPath/help/axt.html.

The alignments were produced by the blastz alignment program, which 
is available from Webb Miller's lab at Penn State University 
(http://www.bx.psu.edu/miller_lab/). The blastz scoring matrix used was:

          A    C    G    T
    A    91 -114  -31 -123
    C  -114  100 -125  -31
    G   -31 -125  100 -114
    T  -123  -31 -114   91

with a gap open penalty of 400 and a gap extension penalty of 30.  The 
minimum score for an alignment to be kept was 3000 for the first pass  
and 2200 for the second pass, which restricted the search space to the 
regions between two alignments found in the first pass.  

Each chromosome was divided into 10,010,000 base chunks with 10,000
bases of overlap.  

The .lav format blastz output, which does not include the sequence, was
converted to .axt with lavToAxt. 

Chains produced by axtChain were also filtered with a minimum score of 5000 
and then chainAntiRepeat was applied to remove chains that are primarily the
result of repeats and degenerate DNA.

The axtNet alignments were processed with chainNet, netSyntenic, 
and netClass written by Jim Kent at UCSC.

----------------------------------------------------------------
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/hg17/vsBosTau1/. To download multiple 
files, use the "mget" command:

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

All the files in this directory are freely available for public use. 
Please review the restrictions on the use of the cow assembly data at
http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html.

--------------------------------------------------------------------
References

Chiaromonte, F., Yap, V.B., and Miller, W.  Scoring pairwise genomic 
sequence alignments.  Pac Symp Biocomput 2002;115-26.

Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. 
Evolution's cauldron: Duplication, deletion, and rearrangement in the 
mouse and human genomes.  Proc Natl Acad Sci USA 100(20):11484-11489 
Sep 30 2003.

Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., 
Haussler, D., and Miller, W.  Human-mouse alignments with BLASTZ</A>. 
Genome Res. 13(1):103-7 (2003).
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