This directory contains alignments of the mouse assembly 
(mm5, May 2004) to the zebrafish assembly (danRer1, Nov. 2003).

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. 

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

  - mouse.net.zip: "net" file that describes rearrangements between the 
    species and the best mouse 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  -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

For chaining, the axtChain linearGap option was used to specify gap 
penalties:

tablesize   11
smallSize   111
position    1    2    3   11   111   2111  12111  32111  72111  152111  252111
qGap      325  360  400  450   600   1100   3600   7600  15600   31600   56600
tGap      325  360  400  450   600   1100   3600   7600  15600   31600   56600
bothGap   625  660  700  750   900   1400   4000   8000  16000   32000   57000


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/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 
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. 

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