This directory contains the Mar. 2007 assembly of the tetraodon genome
(tetNig2, Genoscope Tetraodon v8.0 (NCBI project 12350, CAAE01000000)),
as well as repeat annotations and GenBank sequences.
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:
tetNig2.2bit - contains the complete tetraodon/tetNig2 genome sequence
in the 2bit file format. The utility program, twoBitToFa (available
from the kent src tree), can be used to extract .fa file(s) from
this file. A pre-compiled version of the command line tool can be
found at:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
See also:
http://genome.ucsc.edu/admin/cvs.html
http://genome.ucsc.edu/admin/jk-install.html
chromAgp.tar.gz - Description of how the assembly was generated from
fragments, unpacking to one file per chromosome.
chromFa.tar.gz - The assembly sequence in one file per 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.
chromFaMasked.tar.gz - The assembly sequence in one file per chromosome.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
chromOut.tar.gz - RepeatMasker .out files (one file per chromosome).
RepeatMasker was run with the -s (sensitive) setting.
Repeat masker version: June 4 2009 (open-3-2-8)
Library release 20090604
chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED 5+
format (one file per chromosome).
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Tetraodon mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
xenoMrna.fa.gz - GenBank mRNAs from species other than that of
the genome. This sequence data is updated once a week via automatic
GenBank updates.
tetNig2.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
tetNig2.chromAlias.txt - sequence name alias file, one line
for each sequence name. First column is sequence name followed by
tab separated alias names.
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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
[username: anonymous, password: your email address], then cd to the
directory goldenPath/tetNig2/bigZips. 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/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/tetNig2/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/tetNig2/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/tetNig2/bigZips/chromFa.tar.gz'
-O chromFa.tar.gz
To unpack the *.tar.gz files:
tar xvzf <file>.tar.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 -
chromAgp.tar.gz 2010-01-06 16:29 393K
chromFa.tar.gz 2010-01-06 16:30 96M
chromFaMasked.tar.gz 2010-01-06 16:32 81M
chromOut.tar.gz 2010-01-06 16:29 4.3M
chromTrf.tar.gz 2010-01-06 16:32 1.8M
genes/ 2020-10-02 13:39 -
md5sum.txt 2010-05-20 16:08 301
mrna.fa.gz 2019-10-16 16:35 30M
mrna.fa.gz.md5 2019-10-16 16:35 45
tetNig2.2bit 2009-08-07 12:27 98M
tetNig2.chrom.sizes 2009-08-06 10:29 415
tetNig2.chromAlias.bb 2022-09-08 14:17 41K
tetNig2.chromAlias.txt 2022-09-08 14:17 305
tetNig2.fa.gz 2020-01-23 02:26 96M
upstream1000.fa.gz 2019-10-16 16:46 769K
upstream1000.fa.gz.md5 2019-10-16 16:46 53
upstream2000.fa.gz 2019-10-16 16:46 1.4M
upstream2000.fa.gz.md5 2019-10-16 16:46 53
upstream5000.fa.gz 2019-10-16 16:46 3.4M
upstream5000.fa.gz.md5 2019-10-16 16:46 53
xenoMrna.fa.gz 2019-10-16 16:45 6.8G
xenoMrna.fa.gz.md5 2019-10-16 16:46 49
xenoRefMrna.fa.gz 2019-10-16 16:46 331M
xenoRefMrna.fa.gz.md5 2019-10-16 16:46 52