This directory contains alignments of the D. pseudoobscura assembly 
(dp2, Aug. 2003, BCM HGSC Freeze 1) to the D. melanogaster assembly (dm2, 
Apr. 2004, BDGP Release 4).

Files in this directory include:

  - 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.

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

  - pseudoobscura.net.gz: "net" file that describes rearrangements between
    the species and the best D. pseudoobscura match to any part of the
    D. melanogaster 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 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 the 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.  

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/dm2/vsDp3/. 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. 

      Name                    Last modified      Size  Description
      Parent Directory                             -   
      md5sum.txt              2005-02-15 08:43  810   
      axtNet/                 2005-02-15 08:42    -   
      pseudoobscura.net.gz    2005-02-15 08:41   10M  
      pseudoobscura.chain.gz  2005-02-15 08:41   10M