This directory contains alignments of the Tetraodon assembly
(tetNig1, Feb. 2004) to the mouse assembly (mm5, May 2004)
in "axt" format. For a description, see
http://genome.ucsc.edu/goldenPath/help/axt.html.
The axt 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 axtNet alignments were processed
with chainNet, netSyntenic, and netClass written by Jim Kent at UCSC.
The blastz scoring matrix used for this alignment was HoxD55.q:
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 restricts the search space
to just 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. 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 so
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
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If you plan to download a large file or multiple files from this
directory, we recommend that 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/mm5/vsTetNig1. 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 -
chr1.axt.gz 08-Sep-2004 08:12 4.8M
chr1_random.axt.gz 08-Sep-2004 08:12 26K
chr2.axt.gz 08-Sep-2004 08:12 8.5M
chr2_random.axt.gz 08-Sep-2004 08:12 323K
chr3.axt.gz 08-Sep-2004 08:12 4.1M
chr3_random.axt.gz 08-Sep-2004 08:12 163K
chr4.axt.gz 08-Sep-2004 08:12 5.1M
chr4_random.axt.gz 08-Sep-2004 08:12 154K
chr5.axt.gz 08-Sep-2004 08:12 5.1M
chr5_random.axt.gz 08-Sep-2004 08:12 102K
chr6.axt.gz 08-Sep-2004 08:12 4.6M
chr6_random.axt.gz 08-Sep-2004 08:12 74K
chr7.axt.gz 08-Sep-2004 08:12 8.8M
chr7_random.axt.gz 08-Sep-2004 08:12 1.1M
chr8.axt.gz 08-Sep-2004 08:12 3.8M
chr8_random.axt.gz 08-Sep-2004 08:12 13K
chr9.axt.gz 08-Sep-2004 08:12 4.9M
chr9_random.axt.gz 08-Sep-2004 08:12 7.9K
chr10.axt.gz 08-Sep-2004 08:12 4.3M
chr10_random.axt.gz 08-Sep-2004 08:12 17K
chr11.axt.gz 08-Sep-2004 08:12 6.7M
chr12.axt.gz 08-Sep-2004 08:12 2.9M
chr12_random.axt.gz 08-Sep-2004 08:12 53K
chr13.axt.gz 08-Sep-2004 08:12 3.1M
chr13_random.axt.gz 08-Sep-2004 08:12 34K
chr14.axt.gz 08-Sep-2004 08:12 3.0M
chr14_random.axt.gz 08-Sep-2004 08:12 25K
chr15.axt.gz 08-Sep-2004 08:12 4.3M
chr15_random.axt.gz 08-Sep-2004 08:12 12K
chr16.axt.gz 08-Sep-2004 08:12 2.3M
chr16_random.axt.gz 08-Sep-2004 08:12 9.5K
chr17.axt.gz 08-Sep-2004 08:12 4.5M
chr17_random.axt.gz 08-Sep-2004 08:12 29K
chr18.axt.gz 08-Sep-2004 08:12 5.9M
chr18_random.axt.gz 08-Sep-2004 08:12 43K
chr19.axt.gz 08-Sep-2004 08:12 3.3M
chr19_random.axt.gz 08-Sep-2004 08:12 612K
chrM.axt.gz 08-Sep-2004 08:12 6.6K
chrUn_random.axt.gz 08-Sep-2004 08:12 2.2M
chrX.axt.gz 08-Sep-2004 08:12 3.6M
chrX_random.axt.gz 08-Sep-2004 08:12 153K
chrY.axt.gz 08-Sep-2004 08:12 571K
chrY_random.axt.gz 08-Sep-2004 08:12 18K
md5sum.txt 09-Sep-2004 19:37 2.1K