This directory contains alignments of the following assemblies:

  - target/reference: Zebrafish (danRer3, May 2005, Sanger Centre, Danio rerio 
    Sequencing Project Zv5)

  - 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

  - danRer3.tetNig1.all.chain.gz: chained blastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - danRer3.tetNig1.net.gz: "net" file that describes rearrangements between 
    the species and the best Tetraodon match to any part of the
    Zebrafish genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - axtNet/*.danRer3.tetNig1.net.axt.gz: chained and netted alignments,
    i.e. the best chains in the Zebrafish 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 danRer3 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 danRer3 sequences larger
than 505,000 bases were split into chunks of 505,000 bases overlapping
by 5,000 bases for alignment.  A similar process was followed for tetNig1,
with chunks of 1000,000,000 overlapping by 0.  Following alignment, the
coordinates of the chunk alignments were corrected by the
blastz-normalizeLav script written by Scott Schwartz of Penn State.

Because the danRer3 chrNA and chrUn chromosomes and the tetNig1 random 
chromosomes are comprised of unordered scaffolds separated by 500 <em>N</em>s
and 1000 <em>N</em>s respectively, the blastz alignments and subsequent 
chaining were first performed on the scaffolds, and the coordinates were then 
lifted up to the chromosome level. This avoided false alignments across the 
<em>N</em>s. The M parameter was set to utilize the Blastz dynamic masking 
functionality. The tetraodon sequence was split into 500 kb contigs for the 
non-random chromosomes (lifted up to the chromosome level after chaining) and 
scaffolds for the random chromosomes. Each chunk of danRer3 sequence was 
aligned with all of the tetNig1 sequence in order for dynamic masking to 
occur. 

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=3000 for the first pass
and L=2200 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=2500.  Other blastz
parameters specifically set for this species pair:
    M=50

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/danRer3/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

Harris, R.S. (2007) Improved pairwise alignment of genomic DNA
Ph.D. Thesis, The Pennsylvania State University

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).