This directory contains alignments of the following assemblies:

  - target/reference: X. tropicalis (xenTro2, Aug. 2005, JGI v4.1)

  - query: Chicken (galGal2, Feb. 2004, Chicken Genome Sequencing Consortium Feb. 2004 release)

Files included in this directory:

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

  - xenTro2.galGal2.all.chain.gz: chained blastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - xenTro2.galGal2.net.gz: "net" file that describes rearrangements between 
    the species and the best Chicken match to any part of the
    X. tropicalis genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - xenTro2.galGal2.net.axt.gz: chained and netted alignments,
    i.e. the best chains in the X. tropicalis 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 .

The chainSwap program was used to translate galGal2-referenced chained blastz
alignments to xenTro2 into xenTro2-referenced chains aligned to galGal2.  See
the download directory goldenPath/galGal2/vsXenTro2/README.txt for more
information about the galGal2-referenced blastz and chaining process.

Chained alignments were processed into nets by the chainNet, netSyntenic,
and netClass programs.
Best-chain alignments in axt format were extracted by the netToAxt program.
All programs run after blastz were 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/xenTro2/vsGalGal2/. 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.

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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).