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.

---------------------------------------------------------------
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 2021-06-13 03:05 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.txt.gz 2021-06-10 16:56 867 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 bigFiles.sql 2021-06-13 03:05 1.4K ensemblSource.sql 2021-05-25 14:53 1.4K grp.sql 2014-03-02 04:18 1.4K ensemblToGeneName.sql 2021-05-25 14:50 1.4K tableDescriptions.sql 2019-07-21 03:43 1.4K chromAlias.sql 2018-08-05 09:35 1.4K ensGtp.sql 2021-05-25 14:50 1.4K 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 2021-06-13 03:05 1.6K gbLoaded.sql 2020-08-20 14:43 1.6K gaze.sql 2010-03-10 13:31 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 2021-06-10 16:56 1.8K mrnaOrientInfo.sql 2019-10-20 12:05 1.8K chainHg19.sql 2010-03-10 13:26 1.8K gc5Base.sql 2010-03-10 13:26 1.9K xenoRefGene.sql 2020-08-20 14:43 1.9K augustusGene.sql 2015-07-26 17:28 1.9K ensGene.sql 2021-05-25 14:50 1.9K 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 2021-06-10 16:56 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 xenoMrna.sql 2020-08-20 14:18 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 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 2021-06-13 03:05 5.0K tableDescriptions.txt.gz 2019-07-21 03:43 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.txt.gz 2021-06-10 16:56 39K 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