This directory contains alignments of the human assembly
(hg17, May 2004) 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 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.
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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/tetNig1/vsHg17/. To download multiple files,
use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
All the tables in this directory are freely available for public use.
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 -
md5sum.txt 2004-09-08 13:58 1.3K
chrUn_random.axt.gz 2004-08-26 13:54 65M
chr21_random.axt.gz 2004-08-26 13:53 479K
chr21.axt.gz 2004-08-26 13:53 873K
chr20.axt.gz 2004-08-26 13:53 273K
chr19.axt.gz 2004-08-26 13:53 1.3M
chr18.axt.gz 2004-08-26 13:53 5.1M
chr17.axt.gz 2004-08-26 13:53 2.1M
chr16.axt.gz 2004-08-26 13:53 3.1M
chr15_random.axt.gz 2004-08-26 13:53 653K
chr15.axt.gz 2004-08-26 13:53 2.0M
chr14.axt.gz 2004-08-26 13:53 1.7M
chr13.axt.gz 2004-08-26 13:53 2.0M
chr12.axt.gz 2004-08-26 13:53 3.1M
chr11.axt.gz 2004-08-26 13:53 2.5M
chr10.axt.gz 2004-08-26 13:53 2.2M
chr9.axt.gz 2004-08-26 13:54 2.4M
chr8.axt.gz 2004-08-26 13:54 3.6M
chr7.axt.gz 2004-08-26 13:54 2.4M
chr6.axt.gz 2004-08-26 13:54 1.1M
chr5.axt.gz 2004-08-26 13:54 2.0M
chr4.axt.gz 2004-08-26 13:54 1.7M
chr3_random.axt.gz 2004-08-26 13:54 25K
chr3.axt.gz 2004-08-26 13:54 3.3M
chr2_random.axt.gz 2004-08-26 13:53 284K
chr2.axt.gz 2004-08-26 13:53 4.5M
chr1_random.axt.gz 2004-08-26 13:53 1.0M
chr1.axt.gz 2004-08-26 13:53 4.5M