This directory contains the Mar. 2007 assembly of the tetraodon genome
(tetNig2, Genoscope Tetraodon v8.0 (NCBI project 12350, CAAE01000000))
in one gzip-compressed FASTA file per chromosome.
This assembly was produced by Genoscope - Centre National de Séquençage
and the Broad Institute.
For more information on the tetraodon genome, see the project website:
http://www.genoscope.cns.fr/spip/
http://www.genoscope.cns.fr/spip/Tetraodon-nigroviridis-a-fish-with.html
http://www.broadinstitute.org/annotation/tetraodon/background.html
Files included in this directory:
- chr*.fa.gz: compressed FASTA sequence of each chromosome.
Repeats from RepeatMasker and Tandem Repeats Finder (with period
of 12 or less) are shown in lower case; non-repeating sequence is
shown in upper case.
RepeatMasker was run with the -s (sensitive) setting.
Repeat masker version: June 4 2009 (open-3-2-8)
Library release 20090604
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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/tetNig2/chromosomes. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Alternate methods to ftp access.
Using an rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/tetNig2/chromosomes/ .
For a single file, e.g. chrM.fa.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/tetNig2/chromosomes/chrM.fa.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/tetNig2/chromosomes/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/tetNig2/chromosomes/chrM.fa.gz'
-O chrM.fa.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
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 2010-01-06 16:33 1.2K
chrM.fa.gz 2010-01-06 16:29 5.5K
chr21_random.fa.gz 2010-01-06 16:29 883K
chr15_random.fa.gz 2010-01-06 16:29 1.0M
chr2_random.fa.gz 2010-01-06 16:29 577K
chr1_random.fa.gz 2010-01-06 16:29 344K
chr21.fa.gz 2010-01-06 16:29 1.5M
chr20.fa.gz 2010-01-06 16:29 970K
chr6.fa.gz 2010-01-06 16:29 1.9M
chr19.fa.gz 2010-01-06 16:29 2.0M
chr15.fa.gz 2010-01-06 16:29 2.0M
chr16.fa.gz 2010-01-06 16:29 2.4M
chr4.fa.gz 2010-01-06 16:29 2.7M
chr14.fa.gz 2010-01-06 16:29 2.9M
chr8.fa.gz 2010-01-06 16:29 2.9M
chr18.fa.gz 2010-01-06 16:29 3.0M
chr9.fa.gz 2010-01-06 16:29 2.9M
chr7.fa.gz 2010-01-06 16:29 3.3M
chr17.fa.gz 2010-01-06 16:29 3.4M
chr11.fa.gz 2010-01-06 16:29 3.4M
chr12.fa.gz 2010-01-06 16:29 3.5M
chr13.fa.gz 2010-01-06 16:29 3.8M
chr10.fa.gz 2010-01-06 16:29 3.7M
chr5.fa.gz 2010-01-06 16:29 3.7M
chr3.fa.gz 2010-01-06 16:29 4.3M
chr2.fa.gz 2010-01-06 16:29 6.1M
chr1.fa.gz 2010-01-06 16:29 6.5M
chrUn_random.fa.gz 2010-01-06 16:28 27M