This directory contains alignments of the tetraodon assembly (tetNig1, Feb 2004)
to the zebrafish assembly (danRer2, June 2004).

Files included in this directory:

  - axtChrom directory: contains the axt alignments generated by blastz,
    in one file per chromosome. Blastz output was converted to lav format, 
    which was then converted to axt format. 

  - tetraTetNig1.chain.gz: chained blastz alignments. The chain format is 
    described in http://genome.ucsc.edu/goldenPath/help/chain.html.

  - tetraTetNig1.net.gz: "net" file that describes rearrangements between the 
    species and the best Tetraodon match to any part of the zebrafish 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 axtChrom 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 -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.

Each zebrafish chromosome was divided into 500,000 base chunks for the blastz
alignments. The Tetraon genome was in contigs in one file and dynamic masking 
was implemented using a threshold of 50 so that any base hit more than 50
times is masked. The .lav format blastz output, which does not include the
sequence, was converted to .axt with lavToAxt. Chains were produced by 
axtChain, filtered with a minimum score of 5000 and then chainAntiRepeat 
was applied to remove chains that are primarily the result of repeats 
and degenerate DNA.

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/danRer2/vsTetNig1/. 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 Zv4 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                             -   
      axtChrom/               2005-05-16 15:39    -   
      md5sum.txt              2005-05-16 15:42  110   
      tetraTetNig1.chain.gz   2005-05-16 15:39   37M  
      tetraTetNig1.net.gz     2005-05-16 15:40   11M