This directory contains alignments of the Fugu assembly
(fr1, Aug. 2002) 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.
- 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.
- fr1.chain.zip: chained blastz alignments. The chain format is
described in http://genome.ucsc.edu/goldenPath/help/chain.html.
- fr1.net.zip: "net" file that describes rearrangements between the
species and the best Fugu match to any part of the zebrafish 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 -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.
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/danRer1/fr1/. 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 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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