This directory contains alignments of the Fugu assembly
(fr1, Aug. 2002) to the Tetraodon assembly (tetNig1, Feb. 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.
- 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 Tetraodon 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 8000 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 10,010,000 base chunks for the blastz
alignments. The .lav format blastz output, which does not include
the sequence, was converted to .axt with lavToAxt. There are no
lineage-specific repeats available for these two fish; therefore, none
were used in the blastz alignments.
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/tetNig1/vsFr1/. 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.
The Tetraodon sequence has been freely provided by Genoscope before
publication for use in the UCSC Genome Browser with the following
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, provided that the Genoscope is properly acknowledged.
3. Genoscope reserves the right to publish the initial large-scale analyses
of the dataset, including large-scale identification of regions of
evolutionary conservation and large-scale genomic assembly. Large-scale
refers to regions with size on the order of a Tetraodon chromosome (that
is, 5 Mb or more).
4. Any redistribution of the data should carry this notice.
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80