This directory contains a dump of the UCSC genome annotation database for
the Mar. 2007 assembly of the tetraodon genome
(tetNig2, Genoscope Tetraodon v8.0 (NCBI project 12350, CAAE01000000)).
The annotations were generated by UCSC and collaborators worldwide.
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 (updated nightly):
- *.sql files: the MySQL commands used to create the tables
- *.txt.gz files: the database tables in a tab-delimited format
compressed with gzip.
To see descriptions of the tables underlying Genome Browser annotation
tracks, select the table in the Table Browser:
http://genome.ucsc.edu/cgi-bin/hgTables?db=tetNig2
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
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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/tetNig2/database/. 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/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/tetNig2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/tetNig2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/tetNig2/database/gc5BaseBw.txt.gz'
-O gc5BaseBw.txt.gz
Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.cse.ucsc.edu/gbdb/
To uncompress the *.txt.gz files:
gunzip <table>.txt.gz
The tables can be loaded directly from the .txt.gz compressed file.
It is not necessary to uncompress them to load into a database,
as shown in the example below.
To load one of the tables directly into your local mirror database,
for example the table chromInfo:
## create table from the sql definition
$ hgsql tetNig2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql tetNig2 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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 -
bigFiles.txt.gz 2024-04-21 03:07 33
chromAlias.txt.gz 2018-08-05 09:35 178
grp.txt.gz 2014-03-02 04:18 199
chromInfo.txt.gz 2010-03-10 13:35 274
cytoBandIdeo.txt.gz 2013-04-28 22:33 473
hgFindSpec_pushedout.txt.gz 2021-12-27 12:23 877
hgFindSpec.txt.gz 2023-03-28 13:53 918
gazePep.sql 2010-03-10 13:34 1.3K
history.txt.gz 2010-03-10 13:26 1.3K
chromInfo.sql 2010-03-10 13:35 1.3K
ensPep.sql 2021-05-25 14:53 1.3K
ensemblSource.sql 2021-05-25 14:53 1.4K
grp.sql 2014-03-02 04:18 1.4K
bigFiles.sql 2024-04-21 03:07 1.4K
ensemblToGeneName.sql 2021-05-25 14:50 1.4K
chromAlias.sql 2018-08-05 09:35 1.4K
ensGtp.sql 2021-05-25 14:50 1.4K
tableDescriptions.sql 2024-04-20 02:04 1.5K
chainFr3Link.sql 2012-05-28 15:09 1.5K
chainDanRer7Link.sql 2011-03-24 09:25 1.5K
chainGasAcu1Link.sql 2010-03-10 13:34 1.5K
chainOryLat2Link.sql 2010-03-10 13:34 1.5K
microsat.sql 2015-08-24 02:42 1.5K
windowmaskerSdust.sql 2010-03-10 13:26 1.5K
cytoBandIdeo.sql 2013-04-28 22:33 1.5K
chainHg19Link.sql 2010-03-10 13:30 1.5K
chainMm10Link.sql 2013-10-27 22:09 1.5K
chainGalGal6Link.sql 2019-01-20 20:24 1.5K
history.sql 2010-03-10 13:26 1.6K
tableList.sql 2024-04-21 03:07 1.6K
gaze.sql 2010-03-10 13:31 1.6K
gbLoaded.sql 2020-08-20 14:43 1.6K
cpgIslandExt.sql 2010-03-10 13:27 1.6K
gap.sql 2010-03-10 13:26 1.6K
chainFr3.sql 2012-05-28 15:09 1.6K
chainDanRer7.sql 2011-03-24 09:27 1.6K
chainGasAcu1.sql 2010-03-10 13:33 1.6K
chainOryLat2.sql 2010-03-10 13:26 1.6K
genscan.sql 2013-12-10 06:25 1.7K
tRNAs.sql 2012-04-16 05:37 1.7K
chainMm10.sql 2013-10-27 22:09 1.7K
chainGalGal6.sql 2019-01-20 20:24 1.7K
gold.sql 2010-03-10 13:26 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 20:09 1.7K
xenoRefFlat.sql 2020-08-20 14:43 1.7K
hgFindSpec.sql 2023-03-28 13:53 1.8K
mrnaOrientInfo.sql 2019-10-20 12:05 1.8K
chainHg19.sql 2010-03-10 13:26 1.8K
hgFindSpec_pushedout.sql 2021-12-27 12:23 1.8K
gc5Base.sql 2010-03-10 13:26 1.9K
augustusGene.sql 2015-07-26 17:28 1.9K
ensGene.sql 2021-05-25 14:50 1.9K
xenoRefGene.sql 2020-08-20 14:43 2.0K
nestedRepeats.sql 2010-03-10 13:27 2.0K
netFr3.sql 2012-05-28 15:09 2.0K
netDanRer7.sql 2011-03-24 09:25 2.0K
netGasAcu1.sql 2010-03-10 13:30 2.0K
netOryLat2.sql 2010-03-10 13:28 2.0K
simpleRepeat.sql 2010-03-10 13:28 2.0K
trackDb.sql 2023-03-28 13:53 2.1K
trackDb_pushedout.sql 2021-12-27 12:23 2.1K
netMm10.sql 2013-10-27 22:09 2.1K
chr1_mrna.sql 2016-07-03 09:13 2.1K
chr2_mrna.sql 2016-07-03 09:14 2.1K
chr3_mrna.sql 2016-07-03 09:15 2.1K
chr4_mrna.sql 2019-10-20 12:03 2.1K
chr5_mrna.sql 2016-07-03 09:13 2.1K
chr6_mrna.sql 2016-07-03 09:14 2.1K
chr7_mrna.sql 2016-07-03 09:15 2.1K
chr8_mrna.sql 2016-07-03 09:14 2.1K
chr9_mrna.sql 2016-12-04 09:06 2.1K
chrM_mrna.sql 2016-07-03 09:13 2.1K
chr10_mrna.sql 2016-07-03 09:13 2.1K
chr11_mrna.sql 2016-07-03 09:14 2.1K
chr12_mrna.sql 2016-07-03 09:13 2.1K
chr13_mrna.sql 2016-07-03 09:13 2.1K
chr14_mrna.sql 2016-07-03 09:13 2.1K
chr15_mrna.sql 2016-07-03 09:14 2.1K
chr16_mrna.sql 2016-12-04 09:06 2.1K
chr17_mrna.sql 2016-07-03 09:13 2.1K
chr18_mrna.sql 2016-07-03 09:14 2.1K
chr19_mrna.sql 2016-07-03 09:14 2.1K
chr20_mrna.sql 2016-07-03 09:13 2.1K
chr21_mrna.sql 2016-07-03 09:15 2.1K
netGalGal6.sql 2019-01-20 20:24 2.1K
all_mrna.sql 2019-10-20 12:03 2.1K
chr1_random_mrna.sql 2016-07-03 09:15 2.1K
chr2_random_mrna.sql 2016-07-03 09:13 2.1K
chr15_random_mrna.sql 2016-07-03 09:15 2.1K
chr21_random_mrna.sql 2016-07-03 09:13 2.1K
chrUn_random_mrna.sql 2016-07-03 09:15 2.1K
xenoMrna.sql 2020-08-20 14:18 2.1K
xenoRefSeqAli.sql 2020-08-20 14:43 2.1K
blastHg18KG.sql 2010-03-10 13:27 2.3K
netHg19.sql 2010-03-10 13:26 2.3K
chrM_mrna.txt.gz 2016-07-03 09:13 4.3K
tableList.txt.gz 2024-04-21 03:07 5.2K
tableDescriptions.txt.gz 2024-04-20 02:04 5.8K
chr1_random_mrna.txt.gz 2016-07-03 09:15 8.7K
tRNAs.txt.gz 2012-04-16 05:37 13K
gbLoaded.txt.gz 2020-08-20 14:43 15K
chr2_random_mrna.txt.gz 2016-07-03 09:13 19K
chr20_mrna.txt.gz 2016-07-03 09:13 24K
chr15_random_mrna.txt.gz 2016-07-03 09:15 31K
chr21_random_mrna.txt.gz 2016-07-03 09:13 34K
trackDb_pushedout.txt.gz 2021-12-27 12:23 40K
trackDb.txt.gz 2023-03-28 13:53 42K
chr19_mrna.txt.gz 2016-07-03 09:14 48K
nestedRepeats.txt.gz 2010-03-10 13:27 52K
ensemblSource.txt.gz 2021-05-25 14:53 64K
chr6_mrna.txt.gz 2016-07-03 09:14 68K
chr21_mrna.txt.gz 2016-07-03 09:15 77K
chr17_mrna.txt.gz 2016-07-03 09:13 97K
chr15_mrna.txt.gz 2016-07-03 09:14 103K
chr12_mrna.txt.gz 2016-07-03 09:13 115K
chr10_mrna.txt.gz 2016-07-03 09:13 123K
chr8_mrna.txt.gz 2016-07-03 09:14 125K
chr4_mrna.txt.gz 2019-10-20 12:03 127K
chr9_mrna.txt.gz 2016-12-04 09:06 127K
chr11_mrna.txt.gz 2016-07-03 09:14 130K
ensemblToGeneName.txt.gz 2021-05-25 14:50 130K
chr14_mrna.txt.gz 2016-07-03 09:13 140K
chr7_mrna.txt.gz 2016-07-03 09:15 144K
chr16_mrna.txt.gz 2016-12-04 09:06 156K
chr18_mrna.txt.gz 2016-07-03 09:14 165K
ensGtp.txt.gz 2021-05-25 14:50 217K
chr2_mrna.txt.gz 2016-07-03 09:14 219K
microsat.txt.gz 2015-08-24 02:42 223K
chr5_mrna.txt.gz 2016-07-03 09:13 236K
chr13_mrna.txt.gz 2016-07-03 09:13 242K
chr1_mrna.txt.gz 2016-07-03 09:13 281K
gold.txt.gz 2010-03-10 13:26 297K
chr3_mrna.txt.gz 2016-07-03 09:15 335K
gap.txt.gz 2010-03-10 13:26 437K
cpgIslandExt.txt.gz 2010-03-10 13:27 774K
mrnaOrientInfo.txt.gz 2019-10-20 12:05 876K
cpgIslandExtUnmasked.txt.gz 2014-06-01 20:09 1.0M
chrUn_random_mrna.txt.gz 2016-07-03 09:15 1.1M
genscan.txt.gz 2013-12-10 06:25 1.2M
gc5Base.txt.gz 2010-03-10 13:26 1.4M
gaze.txt.gz 2010-03-10 13:31 1.8M
ensGene.txt.gz 2021-05-25 14:50 2.1M
augustusGene.txt.gz 2015-07-26 17:28 2.5M
blastHg18KG.txt.gz 2010-03-10 13:27 2.8M
simpleRepeat.txt.gz 2010-03-10 13:28 3.5M
chainMm10.txt.gz 2013-10-27 22:09 3.9M
all_mrna.txt.gz 2019-10-20 12:03 4.2M
netMm10.txt.gz 2013-10-27 22:09 4.7M
chainGalGal6.txt.gz 2019-01-20 20:24 4.9M
netHg19.txt.gz 2010-03-10 13:26 5.0M
netGalGal6.txt.gz 2019-01-20 20:24 5.1M
gazePep.txt.gz 2010-03-10 13:34 6.1M
chainHg19.txt.gz 2010-03-10 13:26 6.9M
ensPep.txt.gz 2021-05-25 14:53 6.9M
netDanRer7.txt.gz 2011-03-24 09:25 7.6M
netGasAcu1.txt.gz 2010-03-10 13:31 9.8M
netOryLat2.txt.gz 2010-03-10 13:29 11M
chainFr3.txt.gz 2012-05-28 15:09 12M
netFr3.txt.gz 2012-05-28 15:09 12M
windowmaskerSdust.txt.gz 2010-03-10 13:26 15M
chainGasAcu1.txt.gz 2010-03-10 13:33 16M
xenoRefSeqAli.txt.gz 2020-08-20 14:43 18M
xenoRefFlat.txt.gz 2020-08-20 14:43 20M
chainOryLat2.txt.gz 2010-03-10 13:26 21M
xenoRefGene.txt.gz 2020-08-20 14:43 22M
chainDanRer7.txt.gz 2011-03-24 09:28 24M
chainMm10Link.txt.gz 2013-10-27 22:09 28M
chainGalGal6Link.txt.gz 2019-01-20 20:24 34M
chainHg19Link.txt.gz 2010-03-10 13:30 42M
chainGasAcu1Link.txt.gz 2010-03-10 13:34 83M
chainDanRer7Link.txt.gz 2011-03-24 09:26 88M
chainFr3Link.txt.gz 2012-05-28 15:10 106M
chainOryLat2Link.txt.gz 2010-03-10 13:35 128M
xenoMrna.txt.gz 2020-08-20 14:18 196M