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 - xenoMrna.txt.gz 2020-08-20 14:18 196M chainOryLat2Link.txt.gz 2010-03-10 13:35 128M chainFr3Link.txt.gz 2012-05-28 15:10 106M chainDanRer7Link.txt.gz 2011-03-24 09:26 88M chainGasAcu1Link.txt.gz 2010-03-10 13:34 83M chainHg19Link.txt.gz 2010-03-10 13:30 42M chainGalGal6Link.txt.gz 2019-01-20 20:24 34M chainMm10Link.txt.gz 2013-10-27 22:09 28M chainDanRer7.txt.gz 2011-03-24 09:28 24M xenoRefGene.txt.gz 2020-08-20 14:43 22M chainOryLat2.txt.gz 2010-03-10 13:26 21M xenoRefFlat.txt.gz 2020-08-20 14:43 20M xenoRefSeqAli.txt.gz 2020-08-20 14:43 18M chainGasAcu1.txt.gz 2010-03-10 13:33 16M windowmaskerSdust.txt.gz 2010-03-10 13:26 15M netFr3.txt.gz 2012-05-28 15:09 12M chainFr3.txt.gz 2012-05-28 15:09 12M netOryLat2.txt.gz 2010-03-10 13:29 11M netGasAcu1.txt.gz 2010-03-10 13:31 9.8M netDanRer7.txt.gz 2011-03-24 09:25 7.6M ensPep.txt.gz 2021-05-25 14:53 6.9M chainHg19.txt.gz 2010-03-10 13:26 6.9M gazePep.txt.gz 2010-03-10 13:34 6.1M netGalGal6.txt.gz 2019-01-20 20:24 5.1M netHg19.txt.gz 2010-03-10 13:26 5.0M chainGalGal6.txt.gz 2019-01-20 20:24 4.9M netMm10.txt.gz 2013-10-27 22:09 4.7M all_mrna.txt.gz 2019-10-20 12:03 4.2M chainMm10.txt.gz 2013-10-27 22:09 3.9M simpleRepeat.txt.gz 2010-03-10 13:28 3.5M blastHg18KG.txt.gz 2010-03-10 13:27 2.8M augustusGene.txt.gz 2015-07-26 17:28 2.5M ensGene.txt.gz 2021-05-25 14:50 2.1M gaze.txt.gz 2010-03-10 13:31 1.8M gc5Base.txt.gz 2010-03-10 13:26 1.4M genscan.txt.gz 2013-12-10 06:25 1.2M chrUn_random_mrna.txt.gz 2016-07-03 09:15 1.1M cpgIslandExtUnmasked.txt.gz 2014-06-01 20:09 1.0M mrnaOrientInfo.txt.gz 2019-10-20 12:05 876K cpgIslandExt.txt.gz 2010-03-10 13:27 774K gap.txt.gz 2010-03-10 13:26 437K chr3_mrna.txt.gz 2016-07-03 09:15 335K gold.txt.gz 2010-03-10 13:26 297K chr1_mrna.txt.gz 2016-07-03 09:13 281K chr13_mrna.txt.gz 2016-07-03 09:13 242K chr5_mrna.txt.gz 2016-07-03 09:13 236K microsat.txt.gz 2015-08-24 02:42 223K chr2_mrna.txt.gz 2016-07-03 09:14 219K ensGtp.txt.gz 2021-05-25 14:50 217K chr18_mrna.txt.gz 2016-07-03 09:14 165K chr16_mrna.txt.gz 2016-12-04 09:06 156K chr7_mrna.txt.gz 2016-07-03 09:15 144K chr14_mrna.txt.gz 2016-07-03 09:13 140K ensemblToGeneName.txt.gz 2021-05-25 14:50 130K chr11_mrna.txt.gz 2016-07-03 09:14 130K chr9_mrna.txt.gz 2016-12-04 09:06 127K chr4_mrna.txt.gz 2019-10-20 12:03 127K chr8_mrna.txt.gz 2016-07-03 09:14 125K chr10_mrna.txt.gz 2016-07-03 09:13 123K chr12_mrna.txt.gz 2016-07-03 09:13 115K chr15_mrna.txt.gz 2016-07-03 09:14 103K chr17_mrna.txt.gz 2016-07-03 09:13 97K chr21_mrna.txt.gz 2016-07-03 09:15 77K chr6_mrna.txt.gz 2016-07-03 09:14 68K ensemblSource.txt.gz 2021-05-25 14:53 64K nestedRepeats.txt.gz 2010-03-10 13:27 52K chr19_mrna.txt.gz 2016-07-03 09:14 48K trackDb.txt.gz 2023-03-28 13:53 42K trackDb_pushedout.txt.gz 2021-12-27 12:23 40K chr21_random_mrna.txt.gz 2016-07-03 09:13 34K chr15_random_mrna.txt.gz 2016-07-03 09:15 31K chr20_mrna.txt.gz 2016-07-03 09:13 24K chr2_random_mrna.txt.gz 2016-07-03 09:13 19K gbLoaded.txt.gz 2020-08-20 14:43 15K tRNAs.txt.gz 2012-04-16 05:37 13K chr1_random_mrna.txt.gz 2016-07-03 09:15 8.7K tableDescriptions.txt.gz 2024-03-23 02:04 5.8K tableList.txt.gz 2024-03-24 03:09 5.2K chrM_mrna.txt.gz 2016-07-03 09:13 4.3K netHg19.sql 2010-03-10 13:26 2.3K blastHg18KG.sql 2010-03-10 13:27 2.3K xenoRefSeqAli.sql 2020-08-20 14:43 2.1K xenoMrna.sql 2020-08-20 14:18 2.1K chrUn_random_mrna.sql 2016-07-03 09:15 2.1K chr21_random_mrna.sql 2016-07-03 09:13 2.1K chr15_random_mrna.sql 2016-07-03 09:15 2.1K chr2_random_mrna.sql 2016-07-03 09:13 2.1K chr1_random_mrna.sql 2016-07-03 09:15 2.1K all_mrna.sql 2019-10-20 12:03 2.1K netGalGal6.sql 2019-01-20 20:24 2.1K chr21_mrna.sql 2016-07-03 09:15 2.1K chr20_mrna.sql 2016-07-03 09:13 2.1K chr19_mrna.sql 2016-07-03 09:14 2.1K chr18_mrna.sql 2016-07-03 09:14 2.1K chr17_mrna.sql 2016-07-03 09:13 2.1K chr16_mrna.sql 2016-12-04 09:06 2.1K chr15_mrna.sql 2016-07-03 09:14 2.1K chr14_mrna.sql 2016-07-03 09:13 2.1K chr13_mrna.sql 2016-07-03 09:13 2.1K chr12_mrna.sql 2016-07-03 09:13 2.1K chr11_mrna.sql 2016-07-03 09:14 2.1K chr10_mrna.sql 2016-07-03 09:13 2.1K chrM_mrna.sql 2016-07-03 09:13 2.1K chr9_mrna.sql 2016-12-04 09:06 2.1K chr8_mrna.sql 2016-07-03 09:14 2.1K chr7_mrna.sql 2016-07-03 09:15 2.1K chr6_mrna.sql 2016-07-03 09:14 2.1K chr5_mrna.sql 2016-07-03 09:13 2.1K chr4_mrna.sql 2019-10-20 12:03 2.1K chr3_mrna.sql 2016-07-03 09:15 2.1K chr2_mrna.sql 2016-07-03 09:14 2.1K chr1_mrna.sql 2016-07-03 09:13 2.1K netMm10.sql 2013-10-27 22:09 2.1K trackDb_pushedout.sql 2021-12-27 12:23 2.1K trackDb.sql 2023-03-28 13:53 2.1K simpleRepeat.sql 2010-03-10 13:28 2.0K netOryLat2.sql 2010-03-10 13:28 2.0K netGasAcu1.sql 2010-03-10 13:30 2.0K netDanRer7.sql 2011-03-24 09:25 2.0K netFr3.sql 2012-05-28 15:09 2.0K nestedRepeats.sql 2010-03-10 13:27 2.0K xenoRefGene.sql 2020-08-20 14:43 2.0K ensGene.sql 2021-05-25 14:50 1.9K augustusGene.sql 2015-07-26 17:28 1.9K gc5Base.sql 2010-03-10 13:26 1.9K hgFindSpec_pushedout.sql 2021-12-27 12:23 1.8K chainHg19.sql 2010-03-10 13:26 1.8K mrnaOrientInfo.sql 2019-10-20 12:05 1.8K hgFindSpec.sql 2023-03-28 13:53 1.8K xenoRefFlat.sql 2020-08-20 14:43 1.7K cpgIslandExtUnmasked.sql 2014-06-01 20:09 1.7K gold.sql 2010-03-10 13:26 1.7K chainGalGal6.sql 2019-01-20 20:24 1.7K chainMm10.sql 2013-10-27 22:09 1.7K tRNAs.sql 2012-04-16 05:37 1.7K genscan.sql 2013-12-10 06:25 1.7K chainOryLat2.sql 2010-03-10 13:26 1.6K chainGasAcu1.sql 2010-03-10 13:33 1.6K chainDanRer7.sql 2011-03-24 09:27 1.6K chainFr3.sql 2012-05-28 15:09 1.6K gap.sql 2010-03-10 13:26 1.6K cpgIslandExt.sql 2010-03-10 13:27 1.6K gbLoaded.sql 2020-08-20 14:43 1.6K gaze.sql 2010-03-10 13:31 1.6K tableList.sql 2024-03-24 03:09 1.6K history.sql 2010-03-10 13:26 1.6K chainGalGal6Link.sql 2019-01-20 20:24 1.5K chainMm10Link.sql 2013-10-27 22:09 1.5K chainHg19Link.sql 2010-03-10 13:30 1.5K cytoBandIdeo.sql 2013-04-28 22:33 1.5K windowmaskerSdust.sql 2010-03-10 13:26 1.5K microsat.sql 2015-08-24 02:42 1.5K chainOryLat2Link.sql 2010-03-10 13:34 1.5K chainGasAcu1Link.sql 2010-03-10 13:34 1.5K chainDanRer7Link.sql 2011-03-24 09:25 1.5K chainFr3Link.sql 2012-05-28 15:09 1.5K ensGtp.sql 2021-05-25 14:50 1.4K tableDescriptions.sql 2024-03-23 02:04 1.4K chromAlias.sql 2018-08-05 09:35 1.4K ensemblToGeneName.sql 2021-05-25 14:50 1.4K grp.sql 2014-03-02 04:18 1.4K bigFiles.sql 2024-03-24 03:09 1.4K ensemblSource.sql 2021-05-25 14:53 1.4K ensPep.sql 2021-05-25 14:53 1.3K chromInfo.sql 2010-03-10 13:35 1.3K history.txt.gz 2010-03-10 13:26 1.3K gazePep.sql 2010-03-10 13:34 1.3K hgFindSpec.txt.gz 2023-03-28 13:53 918 hgFindSpec_pushedout.txt.gz 2021-12-27 12:23 877 cytoBandIdeo.txt.gz 2013-04-28 22:33 473 chromInfo.txt.gz 2010-03-10 13:35 274 grp.txt.gz 2014-03-02 04:18 199 chromAlias.txt.gz 2018-08-05 09:35 178 bigFiles.txt.gz 2024-03-24 03:09 33