This directory contains alignments of the D. melanogaster assembly 
(dm1, Jan. 2003, BDGP Release 3) to the D. mojavensis assembly (droMoj1, 
Agencourt Bioscience Corporation 11 August 2004).

Files included in this directory:

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

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

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

  - melanogasterNet.axt.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. 

The alignments in the melanogasterNet file 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 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/droMoj1/vsDm1/. 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

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).

      Name                    Last modified      Size  Description
      Parent Directory                             -   
      melanogaster.chain.gz   2004-11-04 19:59  8.1M  
      melanogaster.net.gz     2004-11-05 08:16  9.9M  
      melanogasterNet.axt.gz  2004-11-05 08:45   41M  
      md5sum.txt              2004-11-05 10:14  167