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