This directory contains chained and netted alignments of the 
Fugu assembly (fr1, Aug. 2002) to the zebrafish assembly 
(danRer1, Nov. 2003). These alignments, which show the best 
chains in the genome, with gaps in the best chains filled in 
by next-best chains where possible, 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 -114  -31 -123
      C -114  100 -125  -31
      G  -31 -125  100 -114
      T -123  -31 -114   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 3000 for the first pass  
and 3000 for the second pass, which restricted the search space to the 
regions between two alignments found in the first pass.

The .lav format blastz output, which does not include the sequence, was 
converted to .axt with lavToAxt. 

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/danRer1/fr1/. 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 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 
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. 

      Name                       Last modified      Size  Description
Parent Directory - md5sum.txt 2004-07-26 09:15 1.3K chrM.axt.gz 2004-06-25 08:58 3.7K chr21.axt.gz 2004-06-25 08:56 507K chr25.axt.gz 2004-06-25 08:56 565K chr24.axt.gz 2004-06-25 08:56 758K chr19.axt.gz 2004-06-25 08:56 779K chr13.axt.gz 2004-06-25 08:55 790K chr12.axt.gz 2004-06-25 08:55 812K chr23.axt.gz 2004-06-25 08:56 869K chr15.axt.gz 2004-06-25 08:55 873K chr10.axt.gz 2004-06-25 08:54 902K chr11.axt.gz 2004-06-25 08:55 906K chr18.axt.gz 2004-06-25 08:55 947K chr6.axt.gz 2004-06-25 08:57 1.0M chr9.axt.gz 2004-06-25 08:57 1.0M chr16.axt.gz 2004-06-25 08:55 1.1M chr20.axt.gz 2004-06-25 08:56 1.1M chr4.axt.gz 2004-06-25 08:57 1.1M chr3.axt.gz 2004-06-25 08:56 1.2M chr14.axt.gz 2004-06-25 08:55 1.2M chr2.axt.gz 2004-06-25 08:56 1.2M chr22.axt.gz 2004-06-25 08:56 1.2M chr8.axt.gz 2004-06-25 08:57 1.2M chr17.axt.gz 2004-06-25 08:55 1.3M chr1.axt.gz 2004-06-25 08:54 1.3M chr5.axt.gz 2004-06-25 08:57 1.4M chr7.axt.gz 2004-06-25 08:57 1.7M chrFinished.axt.gz 2004-06-25 08:58 1.8M chrNA.axt.gz 2004-06-25 08:59 7.7M chrUn.axt.gz 2004-06-25 09:00 10M