This directory contains a dump of the UCSC genome annotation database for
the Nov. 2009 (JGI 4.2/xenTro3) assembly of the
Xenopus (Silurana) tropicalis (western clawed frog) genome
(xenTro3, US DOE Joint Genome Institute (JGI-PGF)
(GCA_000004195.1)) from the X. tropicalis Genome Consortium.
The annotations were generated by UCSC and collaborators worldwide.


This assembly was produced by the US DOE Joint Genome Institute (JGI).
For more information on the X. tropicalis genome, please note the
NCBI WGS Traces information:
	http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAMC01
and the project website:
	http://genome.jgi-psf.org/Xentr4/Xentr4.home.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=xenTro3
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/xenTro3/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/xenTro3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/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 xenTro3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql xenTro3 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

==========================================================================
Data use policy from:
    http://genome.jgi-psf.org/Xentr4/Xentr4.download.html

Preliminary drafts of the X. tropicalis sequence are made freely available
before scientific publication by the JGI and the X. tropicalis Genome 
Consortium, 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 if the provider of this data 
   (DOE Joint Genome Institute) is properly acknowledged. 
3. Additional shotgun sequencing is ongoing, and future assembly 
   releases will be made in a timely fashion. We expect to publish an 
   initial analysis of a high quality draft X. tropicalis genome sequence 
   in 2005 (with submission targeted for the spring of 2005) which will 
   include descriptions of the large scale organization of the frog 
   genome as well as genome-scale comparisons of the frog sequence and 
   gene set with those of other animals. Others who would like to 
   coordinate other genome-wide analysis with this work should contact
   Paul Richardson (pmrichardson@lbl.gov), JGI. We welcome a coordinated 
   approach to describing this community resource. 
4. Any redistribution of the data should carry this notice. 
==========================================================================
      Name                         Last modified      Size  Description
Parent Directory - simpleRepeat.sql 2011-11-02 16:50 1.9K simpleRepeat.txt.gz 2011-11-02 16:50 19M cpgIslandExt.sql 2011-11-02 16:50 1.6K cpgIslandExt.txt.gz 2011-11-02 16:50 316K chromInfo.sql 2011-11-02 16:50 1.3K chromInfo.txt.gz 2011-11-02 16:50 94K chainMelGal1Link.sql 2011-11-02 16:51 1.5K chainMelGal1Link.txt.gz 2011-11-02 16:52 26M chainAnoCar2Link.sql 2011-11-02 16:52 1.5K chainAnoCar2Link.txt.gz 2011-11-02 16:56 685M gap.sql 2011-11-02 17:05 1.5K gap.txt.gz 2011-11-02 17:05 2.0M microsat.sql 2011-11-02 17:05 1.4K microsat.txt.gz 2011-11-02 17:05 136K netHg19.sql 2011-11-02 17:05 2.0K netHg19.txt.gz 2011-11-02 17:05 9.2M gold.sql 2011-11-02 17:06 1.6K gold.txt.gz 2011-11-02 17:06 2.8M chainHg19Link.sql 2011-11-02 17:06 1.5K chainHg19Link.txt.gz 2011-11-02 17:08 482M genscan.sql 2011-11-02 17:15 1.6K genscan.txt.gz 2011-11-02 17:15 2.6M history.sql 2011-11-02 17:16 1.5K history.txt.gz 2011-11-02 17:16 1.0K ctgPos2.sql 2011-11-02 17:16 1.5K ctgPos2.txt.gz 2011-11-02 17:16 186K netMelGal1.sql 2011-11-02 17:16 2.0K netMelGal1.txt.gz 2011-11-02 17:16 5.7M blastHg18KG.sql 2011-11-02 17:16 2.1K blastHg18KG.txt.gz 2011-11-02 17:16 2.7M chainDanRer7Link.sql 2011-11-02 17:16 1.5K chainDanRer7Link.txt.gz 2011-11-02 17:19 665M chainMelGal1.sql 2011-11-02 17:29 1.6K chainMelGal1.txt.gz 2011-11-02 17:29 4.0M extFile.sql 2011-11-02 17:29 1.4K extFile.txt.gz 2011-11-02 17:29 79 rmsk.sql 2011-11-02 17:29 1.8K rmsk.txt.gz 2011-11-02 17:29 43M chainDanRer7.sql 2011-11-02 17:30 1.6K chainDanRer7.txt.gz 2011-11-02 17:31 223M chainGalGal3Link.sql 2011-11-02 17:33 1.5K chainGalGal3Link.txt.gz 2011-11-02 17:33 79M netDanRer7.sql 2011-11-02 17:34 2.0K netDanRer7.txt.gz 2011-11-02 17:34 9.7M chainMonDom5Link.sql 2011-11-02 17:41 1.5K chainMonDom5Link.txt.gz 2011-11-02 17:44 769M netAnoCar2.sql 2011-11-02 17:53 2.0K netAnoCar2.txt.gz 2011-11-02 17:53 8.4M chainAnoCar2.sql 2011-11-02 17:53 1.6K chainAnoCar2.txt.gz 2011-11-02 17:53 64M nestedRepeats.sql 2011-11-02 17:54 1.9K nestedRepeats.txt.gz 2011-11-02 17:54 2.9M chainGalGal3.sql 2011-11-02 17:54 1.6K chainGalGal3.txt.gz 2011-11-02 17:54 17M netGalGal3.sql 2011-11-02 17:54 2.0K netGalGal3.txt.gz 2011-11-02 17:54 6.3M netRn4.sql 2011-11-02 17:54 2.0K netRn4.txt.gz 2011-11-02 17:54 7.2M chainHg19.sql 2011-11-02 17:54 1.6K chainHg19.txt.gz 2011-11-02 17:55 124M ucscToEnsembl.sql 2011-11-02 17:56 1.3K ucscToEnsembl.txt.gz 2011-11-02 17:56 97K gc5BaseBw.sql 2011-11-02 17:56 1.2K gc5BaseBw.txt.gz 2011-11-02 17:56 63 chainRn4Link.sql 2011-11-02 17:56 1.5K chainRn4Link.txt.gz 2011-11-02 17:57 285M chainMonDom5.sql 2011-11-02 18:00 1.6K chainMonDom5.txt.gz 2011-11-02 18:01 218M netMonDom5.sql 2011-11-02 18:02 2.0K netMonDom5.txt.gz 2011-11-02 18:02 7.3M windowmaskerSdust.sql 2011-11-02 18:02 1.4K windowmaskerSdust.txt.gz 2011-11-02 18:03 45M chainRn4.sql 2011-11-02 18:03 1.6K chainRn4.txt.gz 2011-11-02 18:03 44M genscanSubopt.sql 2011-11-02 18:03 1.5K genscanSubopt.txt.gz 2011-11-02 18:03 4.3M phastCons9way.sql 2011-12-11 14:36 1.7K phastCons9way.txt.gz 2011-12-11 14:36 14M multiz9wayFrames.sql 2011-12-11 14:36 1.7K multiz9wayFrames.txt.gz 2011-12-11 14:36 20M phyloP9way.sql 2011-12-11 14:36 1.7K phyloP9way.txt.gz 2011-12-11 14:36 14M phastConsElements9way.sql 2011-12-11 14:36 1.5K phastConsElements9way.txt.gz 2011-12-11 14:36 8.1M multiz9way.sql 2011-12-11 14:37 1.5K multiz9way.txt.gz 2011-12-11 14:37 37M multiz9waySummary.sql 2011-12-11 14:37 1.5K multiz9waySummary.txt.gz 2011-12-11 14:37 6.1M tRNAs.sql 2012-04-16 05:38 1.7K tRNAs.txt.gz 2012-04-16 05:38 56K cytoBandIdeo.sql 2013-04-28 22:43 1.5K cytoBandIdeo.txt.gz 2013-04-28 22:43 93K netMm10.sql 2013-10-27 22:20 2.1K netMm10.txt.gz 2013-10-27 22:20 9.2M chainMm10.sql 2013-10-27 22:20 1.7K chainMm10.txt.gz 2013-10-27 22:20 55M chainMm10Link.sql 2013-10-27 22:20 1.5K chainMm10Link.txt.gz 2013-10-27 22:21 370M grp.sql 2014-03-02 04:18 1.3K grp.txt.gz 2014-03-02 04:18 208 cpgIslandExtUnmasked.sql 2014-06-01 20:18 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 20:18 854K augustusGene.sql 2015-07-26 17:28 1.9K augustusGene.txt.gz 2015-07-26 17:28 2.3M estOrientInfo.sql 2016-05-15 11:46 1.8K estOrientInfo.txt.gz 2016-05-15 11:46 14M all_est.sql 2016-05-15 11:46 2.1K all_est.txt.gz 2016-05-15 11:46 53M intronEst.sql 2016-05-15 11:46 2.1K intronEst.txt.gz 2016-05-15 11:46 32M chromAlias.sql 2018-08-05 09:41 1.4K chromAlias.txt.gz 2018-08-05 09:41 92K ensGtp.sql 2019-02-10 03:42 1.4K ensGtp.txt.gz 2019-02-10 03:42 234K ensPep.sql 2019-02-10 03:42 1.3K ensPep.txt.gz 2019-02-10 03:42 6.6M ensemblToGeneName.sql 2019-02-10 03:42 1.4K ensemblToGeneName.txt.gz 2019-02-10 03:42 140K ensGene.sql 2019-02-10 03:42 1.9K ensGene.txt.gz 2019-02-10 03:42 2.1M ensemblSource.sql 2019-02-10 03:42 1.4K ensemblSource.txt.gz 2019-02-10 03:42 73K tableDescriptions.sql 2019-07-21 03:43 1.4K tableDescriptions.txt.gz 2019-07-21 03:43 6.9K mgcFullMrna.sql 2020-03-01 09:24 2.1K mgcFullMrna.txt.gz 2020-03-01 09:24 971K mgcGenes.sql 2020-03-01 09:24 1.9K mgcGenes.txt.gz 2020-03-01 09:24 764K all_mrna.sql 2020-05-11 17:36 2.1K all_mrna.txt.gz 2020-05-11 17:36 1.9M gbLoaded.sql 2020-09-03 10:12 1.6K mrnaOrientInfo.sql 2020-09-03 10:12 1.8K refFlat.sql 2020-09-03 10:12 1.7K refGene.sql 2020-09-03 10:12 1.9K refSeqAli.sql 2020-09-03 10:12 2.1K gbLoaded.txt.gz 2020-09-03 10:12 69K mrnaOrientInfo.txt.gz 2020-09-03 10:12 514K refFlat.txt.gz 2020-09-03 10:12 803K refGene.txt.gz 2020-09-03 10:12 879K refSeqAli.txt.gz 2020-09-03 10:12 942K trackDb.sql 2021-12-27 12:20 2.1K trackDb.txt.gz 2021-12-27 12:20 39K hgFindSpec.sql 2021-12-27 12:20 1.8K hgFindSpec.txt.gz 2021-12-27 12:20 1.0K bigFiles.sql 2022-08-07 03:09 1.4K bigFiles.txt.gz 2022-08-07 03:09 68 tableList.sql 2022-08-07 03:09 1.6K tableList.txt.gz 2022-08-07 03:09 4.0K