This directory contains alignments of the zebrafish assembly 
(danRer2, June 2004) to the mouse assembly (mm5, May 2004).

Files included in this directory:

  - axtChrom/ directory: 

  - axtNet/ directory: contains chained and netted alignments, i.e. the
    best chains in the genome, with gaps in the best chains filled in 
    by next-best chains where possible. 

  - zebrafishDanRer2.chain.gz: chained blastz alignments. The chain format is 
    described in http://genome.ucsc.edu/goldenPath/help/chain.html.

  - zebrafishDanRer2.net.gz: "net" file that describes rearrangements between 
    the species and the best zebrafish match to any part of the mouse genome.  
    The net format is described in 
    http://genome.ucsc.edu/goldenPath/help/net.html.

  - md5sum.txt: checksums of files in this directory

The alignments in the axtNet and axtChrom directories are in "axt" format. 
For a description, see http://genome.ucsc.edu/goldenPath/help/axt.html.

The alignments were produced by the blastz alignment program, which 
is available from Webb Miller's lab at Penn State University 
(http://www.bx.psu.edu/miller_lab/). The blastz scoring matrix 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 400 and a gap extension penalty of 30.  The 
minimum score for an alignment to be kept was 6000 for the first pass  
and 2000 for the second pass, which restricted the search space to the 
regions between two alignments found in the first pass.

Each chromosome was divided into 10,000,000 base chunks for the blastz 
alignments and all repeats for each organism were used as lineage-specific 
repeats. Repeats were detected with Arian Smit's RepeatMasker program 
using species-specific repeat libraries for each genome. The .lav format 
blastz output, which does not include the sequence, was converted to .axt 
with lavToAxt. Low scores can occur using the scoring matrix above and with 
repeats abridged; therefore, alignments were rescored using PSU's restore_rpts 
program and the default scoring 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

For chaining, the axtChain linearGap option was used to specify gap 
penalties:

tablesize   11
smallSize   111
position    1    2    3   11  111  2111  12111  32111  72111  152111  252111
qGap      325  360  400  450  600  1100   3600   7600  15600   31600   56600
tGap      325  360  400  450  600  1100   3600   7600  15600   31600   56600
bothGap   625  660  700  750  900  1400   4000   8000  16000   32000   57000

Chains produced by axtChain were also filtered with a minimum score of 5000
and then chainAntiRepeat was applied to remove chains that are primarily the
result of repeats and degenerate DNA.

The axtNet alignments were processed with chainNet, netSyntenic,
and netClass 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/mm5/vsDanRer2/. To download multiple 
files, use the "mget" command:

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

All the files in this directory are freely usable for any purpose. 
The Zv4 zebrafish sequence data were produced by the Zebrafish Sequencing
Group at the Sanger Institute and can be obtained directly from
ftp://ftp.sanger.ac.uk/pub/zebrafish/. All sequence data are made available
before scientific publication with the understanding that the groups
involved in generating the data intend to publish the initial large-scale
analyses of the dataset. This will include a summary detailing the data that
have beeen generated and key features of the genome identified from genomic
assembly and clone mapping/sequencing. Any redistribution of the data
should carry this notice.

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

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

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 
Sep 30 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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