This directory contains alignments of the zebrafish genome
(danRer1, May 2004) to the X. tropicalis assembly (xenTro1, Oct. 2004). 

Files included in this 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. 

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

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

  - md5sum.txt: checksums of the files in this directory

The alignments in the axtNet directory 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 10,000 for the first pass  
and 2200 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 with 10,000 bases
of overlap. 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/xenTro1/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. 

Preliminary drafts of the X. tropicalis sequence are made freely available
before scientific publication by the JGI and the X. tropicalis Genome 
Consortium, with the following understanding:

1. The data may be freely downloaded, used in analyses, and repackaged 
   in databases. 
2. Users are free to use the data in scientific papers analyzing 
   particular genes and regions if the provider of this data 
   (DOE Joint Genome Institute) is properly acknowledged. 
3. Additional shotgun sequencing is ongoing, and future assembly 
   releases will be made in a timely fashion. We expect to publish an 
   initial analysis of a high quality draft X. tropicalis genome sequence 
   in 2005 (with submission targeted for the spring of 2005) which will 
   include descriptions of the large scale organization of the frog 
   genome as well as genome-scale comparisons of the frog sequence and 
   gene set with those of other animals. Others who would like to 
   coordinate other genome-wide analysis with this work should contact
   Paul Richardson (pmrichardson@lbl.gov), JGI. We welcome a coordinated 
   approach to describing this community resource. 
4. Any redistribution of the data should carry this notice. 

      Name                    Last modified      Size  Description
      Parent Directory                             -   
      axtNet/                 2004-11-22 17:17    -   
      md5sum.txt              2004-11-06 09:23  104   
      zebrafish.chain.gz      2004-11-06 09:01  382M  
      zebrafish.net.gz        2004-11-06 09:02   42M