This directory contains alignments of the following assemblies:

  - target/reference: D. pseudoobscura (dp3, Nov. 2004, FlyBase Release 1.03)

  - query: D. melanogaster (dm2, Apr. 2004, BDGP v. 4 / DHGP v. 3.2)

Files included in this directory:

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

  - dp3.dm2.all.chain.gz: chained blastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - dp3.dm2.net.gz: "net" file that describes rearrangements between 
    the species and the best D. melanogaster match to any part of the
    D. pseudoobscura genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - axtNet/*.dp3.dm2.net.axt.gz: chained and netted alignments,
    i.e. the best chains in the D. pseudoobscura genome, with gaps in the best
    chains filled in by next-best chains where possible.  The axt format is
    described in http://genome.ucsc.edu/goldenPath/help/axt.html .

  - dp3.dm2.over.chain.gz: chained and netted alignments in chain format.

The chainSwap program was used to translate dm2-referenced chained blastz
alignments to dp3 into dp3-referenced chains aligned to dm2.  See
the download directory goldenPath/dm2/vsDp3/README.txt for more
information about the dm2-referenced blastz and chaining process.

Chained alignments were processed into nets by the chainNet, netSyntenic,
and netClass programs. Best chains (.over.chain) were extracted from the
nets and the set of all chained alignments by the netChainSubset program.
Best-chain alignments in axt format were extracted by the netToAxt program.
All programs run after blastz were 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/dp3/vsDm2/. To download multiple files, use the "mget"
command:

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

All files in this directory are freely available for public use.

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

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

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
(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                             -   
      axtNet/                 2005-05-23 09:20    -   
      dp3.dm2.all.chain.gz    2005-05-23 08:57   18M  
      dp3.dm2.net.gz          2005-05-23 09:05   15M  
      dp3.dm2.over.chain.gz   2005-05-23 08:58  6.5M  
      md5sum.txt              2005-05-23 09:20  1.3K