This directory contains alignments of Zebrafish (danRer3, May 2005,
Sanger Centre, Danio rerio Sequencing Project Zv5) to itself.

Files included in this directory:

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

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

The danRer3 assembly was aligned to itself 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 danRer3,
with chunks of 1800,000,000 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. 
The scaffolds from chrNA and chrUn were not aligned as these align to a 
large number of regions causing an excessive number of chains probably 
because these sequences tend to be from highly variable regions.
The M parameter was set to utilize the Blastz dynamic masking
functionality. Each chunk of danRer3 target sequence was aligned with 
all of the danRer3 query sequence in order for dynamic masking to occur.
 
The blastz scoring matrix (Q parameter) used was the default matrix:

           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 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=5000 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.

Chain minimum score: 5000, and linearGap matrix of (medium):
tableSize   11
smallSize  111
position  1   2   3   11  111 2111  12111 32111  72111 152111  252111
qGap    350 425 450  600  900 2900  22900 57900 117900 217900  317900
tGap    350 425 450  600  900 2900  22900 57900 117900 217900  317900
bothGap 750 825 850 1000 1300 3300  23300 58300 118300 218300  318300

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.

----------------------------------------------------------------
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/vsSelf/. 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).

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[TXT]README.txt06-Jan-2006 16:03 3.8K 
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