This directory contains a dump of the UCSC genome annotation 
database for the assembly of the Xenopus tropicalis genome 
from the US DOE Joint Genome Institute (JGI) (xenTro2, Aug. 2005,
JGI v4.1). 

Files included in this directory (updated nightly):

  - *.sql files: the MySQL commands used to create the tables.
    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=xenTro2
    and click the "describe table schema" button.  There is also a "view
    table schema" link on the configuration page for each track.

  - *.txt.gz files: the database tables in a tab-delimited format 
    compressed with gzip. 

---------------------------------------------------------------
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/xenTro2/database/. To download multiple files, 
use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 

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 - gap.sql 2006-06-13 07:13 1.5K gap.txt.gz 2006-06-13 07:13 2.1M chainRn4.sql 2006-06-13 07:13 1.6K chainRn4.txt.gz 2006-06-13 07:14 44M chainRn4Link.sql 2006-06-13 07:14 1.4K chainRn4Link.txt.gz 2006-06-13 07:17 283M chromInfo.sql 2006-06-13 07:20 1.2K chromInfo.txt.gz 2006-06-13 07:20 100K cpgIslandExt.sql 2006-06-13 07:20 1.6K cpgIslandExt.txt.gz 2006-06-13 07:20 858K gc5Base.sql 2006-06-13 07:21 1.7K gc5Base.txt.gz 2006-06-13 07:21 6.4M genscan.sql 2006-06-13 07:21 1.5K genscan.txt.gz 2006-06-13 07:21 2.8M genscanSubopt.sql 2006-06-13 07:21 1.4K genscanSubopt.txt.gz 2006-06-13 07:21 4.6M gold.sql 2006-06-13 07:21 1.6K gold.txt.gz 2006-06-13 07:21 3.1M netRn4.sql 2006-06-13 07:23 2.2K netRn4.txt.gz 2006-06-13 07:23 7.0M rmsk.sql 2006-06-13 07:23 1.8K rmsk.txt.gz 2006-06-13 07:23 46M simpleRepeat.sql 2006-06-13 07:24 1.9K simpleRepeat.txt.gz 2006-06-13 07:24 15M multiz7way.sql 2006-06-21 08:48 1.4K multiz7way.txt.gz 2006-06-21 08:49 21M multiz7wayFrames.sql 2006-06-21 08:49 1.5K multiz7wayFrames.txt.gz 2006-06-21 08:49 6.0M multiz7waySummary.sql 2006-06-21 08:49 1.4K multiz7waySummary.txt.gz 2006-06-21 08:49 6.5M phastCons7way.sql 2006-06-21 08:49 1.7K phastCons7way.txt.gz 2006-06-21 08:50 14M phastConsElements7way.sql 2006-06-21 08:50 1.4K phastConsElements7way.txt.gz 2006-06-21 08:50 6.8M microsat.sql 2006-08-03 07:52 1.3K microsat.txt.gz 2006-08-03 07:52 139K chainGalGal3.sql 2006-08-06 19:48 1.6K chainGalGal3.txt.gz 2006-08-06 19:48 17M chainGalGal3Link.sql 2006-08-06 19:49 1.4K chainGalGal3Link.txt.gz 2006-08-06 19:49 79M netGalGal3.sql 2006-08-06 19:50 2.2K netGalGal3.txt.gz 2006-08-06 19:50 6.3M chainMonDom4.sql 2006-08-11 12:18 1.6K chainMonDom4.txt.gz 2006-08-11 12:21 219M chainMonDom4Link.sql 2006-08-11 12:23 1.4K chainMonDom4Link.txt.gz 2006-08-11 12:34 771M netMonDom4.sql 2006-08-11 12:45 2.2K netMonDom4.txt.gz 2006-08-11 12:45 7.0M chainMm9Link.sql 2007-11-06 18:28 1.4K chainMm9Link.txt.gz 2007-11-06 18:34 291M netMm9.sql 2007-11-06 18:41 2.2K netMm9.txt.gz 2007-11-06 18:41 8.8M chainMm9.sql 2007-11-06 18:41 1.6K chainMm9.txt.gz 2007-11-06 18:42 46M chainHg19.sql 2009-10-04 12:58 1.8K chainHg19.txt.gz 2009-10-04 12:58 126M chainHg19Link.sql 2009-10-04 12:59 1.5K chainHg19Link.txt.gz 2009-10-04 13:01 494M netHg19.sql 2009-10-04 13:04 2.3K netHg19.txt.gz 2009-10-04 13:04 9.3M blastHg18KG.sql 2009-12-20 16:08 2.3K blastHg18KG.txt.gz 2009-12-20 16:08 2.6M history.sql 2010-07-04 19:18 1.6K history.txt.gz 2010-07-04 19:18 732 ensGene.sql 2011-03-15 13:12 1.9K ensGene.txt.gz 2011-03-15 13:12 2.0M ensPep.sql 2011-03-15 13:13 1.3K ensPep.txt.gz 2011-03-15 13:13 5.7M ensGtp.sql 2011-03-15 13:14 1.4K ensGtp.txt.gz 2011-03-15 13:14 235K chainDanRer7Link.sql 2011-03-24 09:31 1.5K chainDanRer7Link.txt.gz 2011-03-24 09:36 652M chainDanRer7.sql 2011-03-24 09:49 1.6K chainDanRer7.txt.gz 2011-03-24 09:51 224M netDanRer7.sql 2011-03-24 09:55 2.0K netDanRer7.txt.gz 2011-03-24 09:55 9.2M chainAnoCar2.sql 2011-10-16 03:59 1.6K chainAnoCar2.txt.gz 2011-10-16 04:00 51M chainAnoCar2Link.sql 2011-10-16 04:00 1.5K chainAnoCar2Link.txt.gz 2011-10-16 04:01 253M netAnoCar2.sql 2011-10-16 04:03 2.0K netAnoCar2.txt.gz 2011-10-16 04:03 9.6M pubsBlatPsl.sql 2012-05-09 13:11 2.1K pubsBlatPsl.txt.gz 2012-05-09 13:11 464K pubsBlat.sql 2012-05-09 13:12 1.9K pubsBlat.txt.gz 2012-05-09 13:12 315K pubsBingBlat.sql 2014-01-26 19:44 2.4K pubsBingBlat.txt.gz 2014-01-26 19:44 544K pubsBingBlatPsl.sql 2014-01-26 19:44 2.2K pubsBingBlatPsl.txt.gz 2014-01-26 19:44 461K grp.sql 2014-03-02 04:18 1.4K grp.txt.gz 2014-03-02 04:18 223 cpgIslandExtUnmasked.sql 2014-06-01 20:18 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 20:18 481K extFile.sql 2014-10-19 15:46 1.5K extFile.txt.gz 2014-10-19 15:46 85 augustusGene.sql 2015-07-26 17:28 1.9K augustusGene.txt.gz 2015-07-26 17:28 2.4M estOrientInfo.sql 2016-05-15 11:45 1.8K estOrientInfo.txt.gz 2016-05-15 11:45 15M intronEst.sql 2016-05-15 11:45 2.1K intronEst.txt.gz 2016-05-15 11:45 32M all_est.sql 2016-05-15 11:45 2.1K all_est.txt.gz 2016-05-15 11:45 55M tableDescriptions.sql 2019-07-21 03:43 1.4K tableDescriptions.txt.gz 2019-07-21 03:43 6.9K mgcGenes.sql 2020-03-01 09:24 1.9K mgcGenes.txt.gz 2020-03-01 09:24 788K mgcFullMrna.sql 2020-03-01 09:24 2.1K mgcFullMrna.txt.gz 2020-03-01 09:24 944K 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 10:13 1.6K mrnaOrientInfo.sql 2020-09-03 10:13 1.8K refFlat.sql 2020-09-03 10:13 1.7K refGene.sql 2020-09-03 10:13 1.9K refSeqAli.sql 2020-09-03 10:13 2.1K xenoRefFlat.sql 2020-09-03 10:13 1.7K xenoRefGene.sql 2020-09-03 10:13 1.9K xenoRefSeqAli.sql 2020-09-03 10:13 2.1K gbLoaded.txt.gz 2020-09-03 10:13 42K mrnaOrientInfo.txt.gz 2020-09-03 10:13 528K refFlat.txt.gz 2020-09-03 10:13 825K refGene.txt.gz 2020-09-03 10:13 901K refSeqAli.txt.gz 2020-09-03 10:13 943K xenoRefFlat.txt.gz 2020-09-03 10:13 23M xenoRefGene.txt.gz 2020-09-03 10:13 26M xenoRefSeqAli.txt.gz 2020-09-03 10:13 24M trackDb.sql 2021-08-02 14:33 2.1K trackDb.txt.gz 2021-08-02 14:33 41K hgFindSpec.sql 2021-08-02 14:33 1.8K hgFindSpec.txt.gz 2021-08-02 14:33 840 tableList.sql 2021-09-19 03:06 1.6K tableList.txt.gz 2021-09-19 03:06 4.5K bigFiles.sql 2021-09-19 03:06 1.4K bigFiles.txt.gz 2021-09-19 03:06 33