This directory contains the Feb. 2004 freeze of the Tetraodon
nigroviridis version 7 (V7) genome assembly (tetNig1) provided by
Genoscope (http://www.genoscope.cns.fr/). This assembly is the result
of a collaboration between Genoscope and the Broad Institute of MIT
and Harvard in Cambridge, MA.
Files included in this directory:
tetNig1.2bit - contains the complete tetraodon/tetNig1 genome sequence
in the 2bit file format. While we are providing the .2bit for
this assembly, we will continue to use the .nib files in
the Genome Browser. 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.zip - Description of how the assembly was generated,
unpacking to one file per chromosome.
chromFa.zip - 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. The main assembly is found in the chrN.fa
files, where N is the name of the chromosome. The chrN_random.fa
files contain clones that are not yet finished or cannot be placed
with certainty at a specific place on the chromosome. In some
cases, including the human HLA region on chromosome 6, the
chrN_random.fa files also contain haplotypes that differ from the
main assembly.
chromFaMasked.zip - The assembly sequence in one file per
chromosome. Repeats are masked by capital Ns; non-repeating
sequence is shown in upper case.
chromOut.zip - RepeatMasker .out file for chromosomes. These were
created by RepeatMasker at the -s sensitive setting.
chromTrf.zip - Tandem Repeats Finder locations, filtered to keep
repeats with period of less than or equal to 12, and translated
into one .bed file per chromosome.
est.fa.gz - Tetraodon ESTs in GenBank. This sequence data is updated
once a week via automatic GenBank updates.
md5sum.txt - Checksums for each of the *.zip files.
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.
tetNig1.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
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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/bigZips/. 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.chrom.sizes 2004-08-17 20:26 422
tetNig1.2bit 2004-08-17 21:10 98M
chromAgp.zip 2004-09-08 08:31 583K
chromOut.zip 2004-09-08 08:31 4.5M
chromFa.zip 2004-09-08 08:34 95M
chromFaMasked.zip 2004-09-08 08:37 92M
chromTrf.zip 2004-09-08 08:37 1.8M
xenoMrna.zip 2005-01-09 23:10 320M
est.fa.gz 2012-01-03 06:44 20
est.fa.gz.md5 2012-01-03 06:44 44
md5sum.txt 2014-05-05 15:31 418
xenoMrna.fa.gz 2016-02-27 18:41 4.9G
xenoMrna.fa.gz.md5 2016-02-27 18:41 49
mrna.fa.gz 2019-10-17 22:30 30M
mrna.fa.gz.md5 2019-10-17 22:30 45
xenoRefMrna.fa.gz 2019-10-17 22:30 331M
xenoRefMrna.fa.gz.md5 2019-10-17 22:30 52
upstream1000.fa.gz 2019-10-17 22:30 1.4M
upstream1000.fa.gz.md5 2019-10-17 22:30 53
upstream2000.fa.gz 2019-10-17 22:30 2.7M
upstream2000.fa.gz.md5 2019-10-17 22:30 53
upstream5000.fa.gz 2019-10-17 22:30 6.4M
upstream5000.fa.gz.md5 2019-10-17 22:30 53
tetNig1.fa.gz 2020-01-23 02:26 95M