This directory contains alignments of the Fugu assembly
(fr1, Aug. 2002) to the Tetraodon assembly (tetNig1, Feb. 2004)
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
understanding:
1. The data may be freely downloaded, used in analyses, and repackaged
in databases.
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.
Name Last modified Size Description
Parent Directory -
chrUn_random.axt 2004-08-31 21:42 577M
chr1.axt 2004-08-31 21:37 56M
chr2.axt 2004-08-31 21:41 50M
chr3.axt 2004-08-31 21:41 38M
chr10.axt 2004-08-31 21:37 31M
chr18.axt 2004-08-31 21:41 29M
chr12.axt 2004-08-31 21:37 29M
chr7.axt 2004-08-31 21:41 29M
chr11.axt 2004-08-31 21:37 28M
chr13.axt 2004-08-31 21:37 28M
chr9.axt 2004-08-31 21:41 26M
chr5.axt 2004-08-31 21:41 26M
chr17.axt 2004-08-31 21:37 25M
chr16.axt 2004-08-31 21:37 24M
chr8.axt 2004-08-31 21:41 22M
chr14.axt 2004-08-31 21:37 22M
chr15.axt 2004-08-31 21:37 18M
chr21.axt 2004-08-31 21:41 15M
chr4.axt 2004-08-31 21:41 14M
chr6.axt 2004-08-31 21:41 13M
chr19.axt 2004-08-31 21:41 12M
chr1_random.axt 2004-08-31 21:41 11M
chr15_random.axt 2004-08-31 21:37 7.5M
chr21_random.axt 2004-08-31 21:41 7.0M
chr20.axt 2004-08-31 21:41 5.5M
chr2_random.axt 2004-08-31 21:41 5.4M
chr3_random.axt 2004-08-31 21:41 1.2M