This directory contains alignments of the zebrafish assembly 
(danRer1, Nov. 2003) to the mouse assembly (mm5, May 2004)
in "axt" format. For a description, see 
http://genome.ucsc.edu/goldenPath/help/axt.html.

The files in this directory contain 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. The alignments are
stored in one file per chromosome. The chain format is described in 
http://genome.ucsc.edu/goldenPath/help/chain.html. The net format 
is described in http://genome.ucsc.edu/goldenPath/help/net.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 a zebrafish repeats library. 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

The axtNet alignments were processed with chainNet, netSyntenic,
and netClass 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/mm5/vsDanRer1/. 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. 

All zebrafish 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).
      Name                       Last modified      Size  Description
Parent Directory - md5sum.txt 2004-09-10 23:33 2.1K chr9_random.axt.gz 2004-08-04 15:07 5.1K chr15_random.axt.gz 2004-08-04 15:06 5.8K chrY_random.axt.gz 2004-08-04 15:07 7.3K chr10_random.axt.gz 2004-08-04 15:06 7.6K chr16_random.axt.gz 2004-08-04 15:06 8.4K chrM.axt.gz 2004-08-04 15:07 9.4K chr19_random.axt.gz 2004-08-04 15:06 9.7K chr18_random.axt.gz 2004-08-04 15:06 10K chr1_random.axt.gz 2004-08-04 15:06 11K chr8_random.axt.gz 2004-08-04 15:07 12K chr6_random.axt.gz 2004-08-04 15:07 17K chr14_random.axt.gz 2004-08-04 15:06 18K chr13_random.axt.gz 2004-08-04 15:06 20K chr17_random.axt.gz 2004-08-04 15:06 25K chr12_random.axt.gz 2004-08-04 15:06 31K chr5_random.axt.gz 2004-08-04 15:07 33K chr3_random.axt.gz 2004-08-04 15:07 44K chrX_random.axt.gz 2004-08-04 15:07 83K chr4_random.axt.gz 2004-08-04 15:07 89K chr2_random.axt.gz 2004-08-04 15:06 125K chr7_random.axt.gz 2004-08-04 15:07 158K chrY.axt.gz 2004-08-04 15:07 588K chrUn_random.axt.gz 2004-08-04 15:07 1.1M chr19.axt.gz 2004-08-04 15:06 1.1M chr18.axt.gz 2004-08-04 15:06 1.1M chr16.axt.gz 2004-08-04 15:06 1.2M chr13.axt.gz 2004-08-04 15:06 1.5M chr15.axt.gz 2004-08-04 15:06 1.5M chr12.axt.gz 2004-08-04 15:06 1.5M chr17.axt.gz 2004-08-04 15:06 1.6M chr14.axt.gz 2004-08-04 15:06 1.7M chr8.axt.gz 2004-08-04 15:07 1.8M chr10.axt.gz 2004-08-04 15:06 1.8M chr6.axt.gz 2004-08-04 15:07 1.9M chr9.axt.gz 2004-08-04 15:07 2.0M chr3.axt.gz 2004-08-04 15:07 2.1M chr4.axt.gz 2004-08-04 15:07 2.2M chr5.axt.gz 2004-08-04 15:07 2.2M chrX.axt.gz 2004-08-04 15:07 2.3M chr7.axt.gz 2004-08-04 15:07 2.4M chr11.axt.gz 2004-08-04 15:06 2.5M chr1.axt.gz 2004-08-04 15:06 2.7M chr2.axt.gz 2004-08-04 15:06 3.3M