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 -
gold.sql 2010-03-10 13:26 1.7K
gold.txt.gz 2010-03-10 13:26 297K
netHg19.sql 2010-03-10 13:26 2.3K
netHg19.txt.gz 2010-03-10 13:26 5.0M
chainHg19.sql 2010-03-10 13:26 1.8K
chainHg19.txt.gz 2010-03-10 13:26 6.9M
gap.sql 2010-03-10 13:26 1.6K
gap.txt.gz 2010-03-10 13:26 437K
gc5Base.sql 2010-03-10 13:26 1.9K
gc5Base.txt.gz 2010-03-10 13:26 1.4M
chainOryLat2.sql 2010-03-10 13:26 1.6K
chainOryLat2.txt.gz 2010-03-10 13:26 21M
history.sql 2010-03-10 13:26 1.6K
history.txt.gz 2010-03-10 13:26 1.3K
windowmaskerSdust.sql 2010-03-10 13:26 1.5K
windowmaskerSdust.txt.gz 2010-03-10 13:26 15M
blastHg18KG.sql 2010-03-10 13:27 2.3K
blastHg18KG.txt.gz 2010-03-10 13:27 2.8M
nestedRepeats.sql 2010-03-10 13:27 2.0K
nestedRepeats.txt.gz 2010-03-10 13:27 52K
cpgIslandExt.sql 2010-03-10 13:27 1.6K
cpgIslandExt.txt.gz 2010-03-10 13:27 774K
simpleRepeat.sql 2010-03-10 13:28 2.0K
simpleRepeat.txt.gz 2010-03-10 13:28 3.5M
netOryLat2.sql 2010-03-10 13:28 2.0K
netOryLat2.txt.gz 2010-03-10 13:29 11M
chainHg19Link.sql 2010-03-10 13:30 1.5K
chainHg19Link.txt.gz 2010-03-10 13:30 42M
netGasAcu1.sql 2010-03-10 13:30 2.0K
netGasAcu1.txt.gz 2010-03-10 13:31 9.8M
gaze.sql 2010-03-10 13:31 1.6K
gaze.txt.gz 2010-03-10 13:31 1.8M
chainGasAcu1.sql 2010-03-10 13:33 1.6K
chainGasAcu1.txt.gz 2010-03-10 13:33 16M
chainGasAcu1Link.sql 2010-03-10 13:34 1.5K
chainGasAcu1Link.txt.gz 2010-03-10 13:34 83M
gazePep.sql 2010-03-10 13:34 1.3K
gazePep.txt.gz 2010-03-10 13:34 6.1M
chainOryLat2Link.sql 2010-03-10 13:34 1.5K
chainOryLat2Link.txt.gz 2010-03-10 13:35 128M
chromInfo.sql 2010-03-10 13:35 1.3K
chromInfo.txt.gz 2010-03-10 13:35 274
netDanRer7.sql 2011-03-24 09:25 2.0K
netDanRer7.txt.gz 2011-03-24 09:25 7.6M
chainDanRer7Link.sql 2011-03-24 09:25 1.5K
chainDanRer7Link.txt.gz 2011-03-24 09:26 88M
chainDanRer7.sql 2011-03-24 09:27 1.6K
chainDanRer7.txt.gz 2011-03-24 09:28 24M
tRNAs.sql 2012-04-16 05:37 1.7K
tRNAs.txt.gz 2012-04-16 05:37 13K
chainFr3.sql 2012-05-28 15:09 1.6K
chainFr3.txt.gz 2012-05-28 15:09 12M
netFr3.sql 2012-05-28 15:09 2.0K
netFr3.txt.gz 2012-05-28 15:09 12M
chainFr3Link.sql 2012-05-28 15:09 1.5K
chainFr3Link.txt.gz 2012-05-28 15:10 106M
cytoBandIdeo.sql 2013-04-28 22:33 1.5K
cytoBandIdeo.txt.gz 2013-04-28 22:33 473
chainMm10.sql 2013-10-27 22:09 1.7K
chainMm10.txt.gz 2013-10-27 22:09 3.9M
chainMm10Link.sql 2013-10-27 22:09 1.5K
chainMm10Link.txt.gz 2013-10-27 22:09 28M
netMm10.sql 2013-10-27 22:09 2.1K
netMm10.txt.gz 2013-10-27 22:09 4.7M
genscan.sql 2013-12-10 06:25 1.7K
genscan.txt.gz 2013-12-10 06:25 1.2M
grp.sql 2014-03-02 04:18 1.4K
grp.txt.gz 2014-03-02 04:18 199
cpgIslandExtUnmasked.sql 2014-06-01 20:09 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 20:09 1.0M
augustusGene.sql 2015-07-26 17:28 1.9K
augustusGene.txt.gz 2015-07-26 17:28 2.5M
microsat.sql 2015-08-24 02:42 1.5K
microsat.txt.gz 2015-08-24 02:42 223K
chr2_random_mrna.sql 2016-07-03 09:13 2.1K
chr2_random_mrna.txt.gz 2016-07-03 09:13 19K
chr5_mrna.sql 2016-07-03 09:13 2.1K
chr5_mrna.txt.gz 2016-07-03 09:13 236K
chr10_mrna.sql 2016-07-03 09:13 2.1K
chr10_mrna.txt.gz 2016-07-03 09:13 123K
chr21_random_mrna.sql 2016-07-03 09:13 2.1K
chr21_random_mrna.txt.gz 2016-07-03 09:13 34K
chr1_mrna.sql 2016-07-03 09:13 2.1K
chr1_mrna.txt.gz 2016-07-03 09:13 281K
chr12_mrna.sql 2016-07-03 09:13 2.1K
chr12_mrna.txt.gz 2016-07-03 09:13 115K
chr14_mrna.sql 2016-07-03 09:13 2.1K
chr14_mrna.txt.gz 2016-07-03 09:13 140K
chr17_mrna.sql 2016-07-03 09:13 2.1K
chr17_mrna.txt.gz 2016-07-03 09:13 97K
chrM_mrna.sql 2016-07-03 09:13 2.1K
chrM_mrna.txt.gz 2016-07-03 09:13 4.3K
chr13_mrna.sql 2016-07-03 09:13 2.1K
chr13_mrna.txt.gz 2016-07-03 09:13 242K
chr20_mrna.sql 2016-07-03 09:13 2.1K
chr20_mrna.txt.gz 2016-07-03 09:13 24K
chr6_mrna.sql 2016-07-03 09:14 2.1K
chr6_mrna.txt.gz 2016-07-03 09:14 68K
chr8_mrna.sql 2016-07-03 09:14 2.1K
chr8_mrna.txt.gz 2016-07-03 09:14 125K
chr11_mrna.sql 2016-07-03 09:14 2.1K
chr11_mrna.txt.gz 2016-07-03 09:14 130K
chr15_mrna.sql 2016-07-03 09:14 2.1K
chr18_mrna.sql 2016-07-03 09:14 2.1K
chr18_mrna.txt.gz 2016-07-03 09:14 165K
chr15_mrna.txt.gz 2016-07-03 09:14 103K
chr2_mrna.sql 2016-07-03 09:14 2.1K
chr2_mrna.txt.gz 2016-07-03 09:14 219K
chr19_mrna.sql 2016-07-03 09:14 2.1K
chr19_mrna.txt.gz 2016-07-03 09:14 48K
chr1_random_mrna.sql 2016-07-03 09:15 2.1K
chr1_random_mrna.txt.gz 2016-07-03 09:15 8.7K
chr3_mrna.sql 2016-07-03 09:15 2.1K
chr3_mrna.txt.gz 2016-07-03 09:15 335K
chr7_mrna.sql 2016-07-03 09:15 2.1K
chr7_mrna.txt.gz 2016-07-03 09:15 144K
chr15_random_mrna.sql 2016-07-03 09:15 2.1K
chr15_random_mrna.txt.gz 2016-07-03 09:15 31K
chr21_mrna.sql 2016-07-03 09:15 2.1K
chr21_mrna.txt.gz 2016-07-03 09:15 77K
chrUn_random_mrna.sql 2016-07-03 09:15 2.1K
chrUn_random_mrna.txt.gz 2016-07-03 09:15 1.1M
chr9_mrna.sql 2016-12-04 09:06 2.1K
chr9_mrna.txt.gz 2016-12-04 09:06 127K
chr16_mrna.sql 2016-12-04 09:06 2.1K
chr16_mrna.txt.gz 2016-12-04 09:06 156K
chromAlias.sql 2018-08-05 09:35 1.4K
chromAlias.txt.gz 2018-08-05 09:35 178
chainGalGal6.sql 2019-01-20 20:24 1.7K
chainGalGal6.txt.gz 2019-01-20 20:24 4.9M
chainGalGal6Link.sql 2019-01-20 20:24 1.5K
chainGalGal6Link.txt.gz 2019-01-20 20:24 34M
netGalGal6.sql 2019-01-20 20:24 2.1K
netGalGal6.txt.gz 2019-01-20 20:24 5.1M
all_mrna.sql 2019-10-20 12:03 2.1K
all_mrna.txt.gz 2019-10-20 12:03 4.2M
chr4_mrna.sql 2019-10-20 12:03 2.1K
chr4_mrna.txt.gz 2019-10-20 12:03 127K
mrnaOrientInfo.sql 2019-10-20 12:05 1.8K
mrnaOrientInfo.txt.gz 2019-10-20 12:05 876K
xenoMrna.sql 2020-08-20 14:18 2.1K
xenoMrna.txt.gz 2020-08-20 14:18 196M
xenoRefGene.sql 2020-08-20 14:43 2.0K
xenoRefGene.txt.gz 2020-08-20 14:43 22M
xenoRefFlat.sql 2020-08-20 14:43 1.7K
xenoRefFlat.txt.gz 2020-08-20 14:43 20M
xenoRefSeqAli.sql 2020-08-20 14:43 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 14:43 18M
gbLoaded.sql 2020-08-20 14:43 1.6K
gbLoaded.txt.gz 2020-08-20 14:43 15K
ensGene.sql 2021-05-25 14:50 1.9K
ensGene.txt.gz 2021-05-25 14:50 2.1M
ensGtp.sql 2021-05-25 14:50 1.4K
ensGtp.txt.gz 2021-05-25 14:50 217K
ensemblToGeneName.sql 2021-05-25 14:50 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:50 130K
ensemblSource.sql 2021-05-25 14:53 1.4K
ensemblSource.txt.gz 2021-05-25 14:53 64K
ensPep.sql 2021-05-25 14:53 1.3K
ensPep.txt.gz 2021-05-25 14:53 6.9M
trackDb.sql 2023-03-28 13:53 2.1K
trackDb.txt.gz 2023-03-28 13:53 42K
hgFindSpec.sql 2023-03-28 13:53 1.8K
hgFindSpec.txt.gz 2023-03-28 13:53 918
tableDescriptions.sql 2024-11-23 02:04 1.5K
tableDescriptions.txt.gz 2024-11-23 02:04 5.8K
tableList.sql 2024-11-24 03:06 1.6K
tableList.txt.gz 2024-11-24 03:06 5.1K
bigFiles.sql 2024-11-24 03:06 1.4K
bigFiles.txt.gz 2024-11-24 03:06 33