This directory contains alignments of the Tetraodon assembly
(tetNig1, Feb. 2004) to the human assembly (hg17, May 2004).
Files included in this directory:
- 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.
- axtTight directory: contains a highly conserved subset of the best
alignments for any part of the human genome.
- tetNig1.chain.gz: chained blastz alignments. The chain format is
described in http://genome.ucsc.edu/goldenPath/help/chain.html.
- tetNig1.net.gz: "net" file that describes rearrangements between the
species and the best Tetraodon match to any part of the human genome.
The net format is described in
http://genome.ucsc.edu/goldenPath/help/net.html.
The alignments in the axtNet and axtTight directories 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 2000 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 10,000,000 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.
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
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 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/hg17/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 available for public use.
--------------------------------------------------------------------
References
Chiaromonte, F., Yap, V.B., and Miller, W. Scoring pairwise genomic
sequence alignments. Pac Symp Biocomput 2002;115-26.
Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.
Evolution's cauldron: Duplication, deletion, and rearrangement in the
mouse and human genomes. Proc Natl Acad Sci USA 100(20):11484-11489
Sep 30 2003.
Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,
Haussler, D., and Miller, W. Human-mouse alignments with BLASTZ</A>.
Genome Res. 13(1):103-7 (2003).
Name Last modified Size Description
Parent Directory -
axtChrom/ 2004-09-08 19:12 -
md5sum.txt 2004-09-14 08:05 96
md5sum.gz 2004-09-14 08:42 144
tetNig1.net.gz 2004-09-14 08:04 6.4M
tetNig1.net.zip 2004-09-08 18:58 6.4M
tetNig1.chain.gz 2004-09-14 08:04 19M
tetNig1.chain.zip 2004-09-08 18:55 19M