This directory contains alignments of the human assembly (hg17, 
May 2004) to the cow assembly (bosTau1, Sep. 2004, BCM HGSC Btau_1.0).

Files included in this directory:

  - axtNet.gz: 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. 

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

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

  - md5sum.txt: checksums of the files in this directory

The alignments in axtNet.gz 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/bosTau1/vsHg17/. 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.
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