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
- 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
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 (firstname.lastname@example.org), JGI. We welcome a coordinated
approach to describing this community resource.
4. Any redistribution of the data should carry this notice.
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