This directory contains alignments of the human assembly (hg17, 
May 2004) to the chimp assembly (panTro1, Nov. 2003).

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. 

  - chimp.net.chain.gz: "net" file that describes rearrangements between the 
    species and the best human match to any part of the chimp 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.

For more information about the chain file format, see
http://genome.ucsc.edu/goldenPath/help/chain.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   100 -300 -150 -300
   C  -300  100 -300 -150
   G  -150 -300  100 -300
   T  -300 -150 -300  100

with a gap open penalty of 400 and a gap extension penalty of 30.  

Each chromosome was divided into 10,000,000 base chunks with 10000 bases
of overlap. The .lav format blastz output, which does not include
the sequence, was converted to .axt with lavToAxt. 

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

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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/panTro1/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.

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References

Harris, R.S. (2007) Improved pairwise alignment of genomic DNA
Ph.D. Thesis, The Pennsylvania State University

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).