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 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

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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. 

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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 - chr10.axt.gz 2004-08-02 19:20 8.9M chr10_random.axt.gz 2004-08-02 19:20 31K chr11.axt.gz 2004-08-02 19:20 12M chr12.axt.gz 2004-08-02 19:20 8.4M chr12_random.axt.gz 2004-08-02 19:20 129K chr13.axt.gz 2004-08-02 19:20 16M chr13_random.axt.gz 2004-08-02 19:20 37K chr14.axt.gz 2004-08-02 19:20 6.4M chr14_random.axt.gz 2004-08-02 19:20 156K chr15.axt.gz 2004-08-02 19:21 17M chr15_random.axt.gz 2004-08-02 19:21 14K chr16.axt.gz 2004-08-02 19:21 6.2M chr16_random.axt.gz 2004-08-02 19:21 33K chr17.axt.gz 2004-08-02 19:22 31M chr17_random.axt.gz 2004-08-02 19:22 123K chr18.axt.gz 2004-08-02 19:22 8.4M chr18_random.axt.gz 2004-08-02 19:22 110K chr19.axt.gz 2004-08-02 19:22 6.7M chr19_random.axt.gz 2004-08-02 19:22 1.2M chr1.axt.gz 2004-08-02 19:22 13M chr1_random.axt.gz 2004-08-02 19:22 46K chr2.axt.gz 2004-08-02 19:23 32M chr2_random.axt.gz 2004-08-02 19:23 1.5M chr3.axt.gz 2004-08-02 19:23 12M chr3_random.axt.gz 2004-08-02 19:23 129K chr4.axt.gz 2004-08-02 19:23 13M chr4_random.axt.gz 2004-08-02 19:23 806K chr5.axt.gz 2004-08-02 19:24 17M chr5_random.axt.gz 2004-08-02 19:24 171K chr6.axt.gz 2004-08-02 19:24 18M chr6_random.axt.gz 2004-08-02 19:24 102K chr7.axt.gz 2004-08-02 19:25 54M chr7_random.axt.gz 2004-08-02 19:25 8.9M chr8.axt.gz 2004-08-02 19:25 9.9M chr8_random.axt.gz 2004-08-02 19:25 42K chr9.axt.gz 2004-08-02 19:26 21M chr9_random.axt.gz 2004-08-02 19:26 36K chrM.axt.gz 2004-08-02 19:26 15K chrUn_random.axt.gz 2004-08-02 19:27 89M chrX.axt.gz 2004-08-02 19:27 16M chrX_random.axt.gz 2004-08-02 19:27 793K chrY.axt.gz 2004-08-02 19:27 6.8M chrY_random.axt.gz 2004-08-02 19:27 18K md5sum.txt 2004-09-10 22:27 2.1K