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.
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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/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.
Name Last modified Size Description
Parent Directory -
axtChrom/ 2004-12-02 13:58 -
md5sum.txt 2004-09-10 22:33 94
mm5.chain.zip 2004-09-10 22:31 97M
mm5.net.zip 2004-09-10 22:31 26M