This directory contains alignments of the Tetraodon assembly
(tetNig1, Feb. 2004) to the mouse assembly (mm5, May 2004).
Files included in this directory:
- axtChrom 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.
- tetNig1.chain.zip: chained blastz alignments. The chain format is
described in http://genome.ucsc.edu/goldenPath/help/chain.html.
- tetNig1.net.zip: "net" file that describes rearrangements between the
species and the best Tetraodon match to any part of the mouse genome.
The net format is described in
http://genome.ucsc.edu/goldenPath/help/net.html.
- md5sum.txt: checksums of the files in this directory
The files in the axtChrom directory are 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
For chaining, the axtChain linearGap option was used to specify gap
penalties:
tablesize 11
smallSize 111
position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000
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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 -
tetNig1.chain.zip 2004-09-09 19:15 13M
tetNig1.net.zip 2004-09-09 19:29 7.8M
md5sum.txt 2004-09-09 19:31 102
axtChrom/ 2004-12-02 13:58 -