This directory contains alignments of the following assemblies:

  - target/reference: Chicken (galGal2, Feb. 2004, Chicken Genome Sequencing Consortium Feb. 2004 release)

  - query: Tetraodon (tetNig1, Feb. 2004, Genoscope and Broad Institute, V7)

Files included in this directory:

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

  - galGal2.tetNig1.all.chain.gz: chained blastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - galGal2.tetNig1.net.gz: "net" file that describes rearrangements between 
    the species and the best Tetraodon match to any part of the
    Chicken genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - axtNet/*.galGal2.tetNig1.net.axt.gz: chained and netted alignments,
    i.e. the best chains in the Chicken 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 galGal2 and tetNig1 assemblies were aligned by the blastz alignment
program, which is available from Webb Miller's lab at Penn State
University (http://www.bx.psu.edu/miller_lab/).  Any sequences larger
than 10,010,000 bases were split into chunks of 10,010,000 bases
overlapping by 10,000 bases for alignment.  Following alignment, the
coordinates of the chunk alignments were corrected by the
blastz-normalizeLav script written by Scott Schwartz of Penn State. 

The blastz scoring matrix (Q parameter) used was:

             A    C    G    T
      A     91  -90  -25 -100
      C    -90  100 -100  -25
      G    -25 -100  100  -90
      T   -100  -25  -90  91

with a gap open penalty of O=400 and a gap extension penalty of E=30.
The minimum score for an alignment to be kept was K=2200 for the first pass
and L=6000 for the second pass, which restricted the search space to the
regions between two alignments found in the first pass.  The minimum
score for alignments to be interpolated between was H=2000.  Other blastz
parameters specifically set for this species pair:
    Y=3400

The .lav format blastz output was translated to the .psl format with
lavToPsl, then chained by the axtChain program.

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/galGal2/vsTetNig1/. 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).

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