This directory contains alignments of the mouse assembly 
(mm5, May 2004) to the zebrafish assembly (danRer1, Nov. 2003)
in "axt" format. For a description, see

The alignments were produced by the blastz alignment program, which 
is available from Webb Miller's lab at Penn State University 
( 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

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, then go to 
the directory goldenPath/danRer1/vsMm5/. To download multiple files, 
use the "mget" command:

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

All the tables in this directory are freely available for public use. 

The Zv3 zebrafish sequence data were produced by the Zebrafish Sequencing 
Group at the Sanger Institute and can be obtained directly from 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. 

      Name                       Last modified      Size  Description
Parent Directory - chrUn.axt.gz 2004-08-05 06:41 139M chrNA.axt.gz 2004-08-05 06:40 155M chrM.axt.gz 2004-08-05 06:38 46K chrFinished.axt.gz 2004-08-05 06:38 14M chr25.axt.gz 2004-08-05 06:38 2.7M chr24.axt.gz 2004-08-05 06:38 4.3M chr23.axt.gz 2004-08-05 06:38 8.4M chr22.axt.gz 2004-08-05 06:38 28M chr21.axt.gz 2004-08-05 06:38 5.0M chr20.axt.gz 2004-08-05 06:38 6.0M chr19.axt.gz 2004-08-05 06:38 6.7M chr18.axt.gz 2004-08-05 06:38 4.6M chr17.axt.gz 2004-08-05 06:38 10M chr16.axt.gz 2004-08-05 06:38 5.6M chr15.axt.gz 2004-08-05 06:37 24M chr14.axt.gz 2004-08-05 06:37 6.5M chr13.axt.gz 2004-08-05 06:37 2.5M chr12.axt.gz 2004-08-05 06:37 5.7M chr11.axt.gz 2004-08-05 06:37 4.2M chr10.axt.gz 2004-08-05 06:37 7.8M chr9.axt.gz 2004-08-05 06:38 5.5M chr8.axt.gz 2004-08-05 06:38 8.6M chr7.axt.gz 2004-08-05 06:38 6.8M chr6.axt.gz 2004-08-05 06:38 6.5M chr5.axt.gz 2004-08-05 06:38 7.6M chr4.axt.gz 2004-08-05 06:38 16M chr3.axt.gz 2004-08-05 06:38 16M chr2.axt.gz 2004-08-05 06:38 6.3M chr1.axt.gz 2004-08-05 06:38 6.7M