This directory contains a dump of the UCSC genome annotation 
database for the October 2004 assembly of the Xenopus tropicalis
genome (xenTro1, Oct. 2004) from the US DOE Joint Genome Institute
(JGI). 

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=xenTro1
    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/xenTro1/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 - all_est.sql 2016-05-15 11:45 2.1K all_est.txt.gz 2016-05-15 11:45 57M all_mrna.sql 2020-05-11 17:36 2.1K all_mrna.txt.gz 2020-05-11 17:36 2.0M augustusGene.sql 2015-07-26 17:28 1.9K augustusGene.txt.gz 2015-07-26 17:28 2.4M bigFiles.sql 2021-05-02 03:10 1.4K bigFiles.txt.gz 2021-05-02 03:10 33 blastHg17KG.sql 2013-10-01 12:48 1.3K blastHg17KG.txt.gz 2005-03-05 05:28 3.2M blatFr1.sql 2013-10-01 12:48 1.3K blatFr1.txt.gz 2004-11-18 12:20 43M chainDanRer1.sql 2013-10-01 12:48 886 chainDanRer1.txt.gz 2004-11-16 09:43 169M chainDanRer1Link.sql 2013-10-01 12:48 585 chainDanRer1Link.txt.gz 2004-11-16 09:50 710M chainGalGal2.sql 2013-10-01 12:48 886 chainGalGal2.txt.gz 2004-11-16 09:56 11M chainGalGal2Link.sql 2013-10-01 12:48 585 chainGalGal2Link.txt.gz 2004-11-16 09:57 63M chainHg18.sql 2013-10-01 12:48 880 chainHg18.txt.gz 2006-04-15 06:39 57M chainHg18Link.sql 2013-10-01 12:48 579 chainHg18Link.txt.gz 2006-04-15 06:36 253M chainMm8.sql 2013-10-01 12:48 812 chainMm8.txt.gz 2006-05-05 06:35 26M chainMm8Link.sql 2013-10-01 12:48 577 chainMm8Link.txt.gz 2006-05-05 06:32 216M chromInfo.sql 2013-10-01 12:48 396 chromInfo.txt.gz 2004-11-16 10:07 131K cpgIslandExt.sql 2013-10-01 12:48 751 cpgIslandExt.txt.gz 2004-11-16 10:07 842K cpgIslandExtUnmasked.sql 2014-06-01 20:17 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 20:17 906K cytoBandIdeo.sql 2018-05-13 08:39 1.5K cytoBandIdeo.txt.gz 2018-05-13 08:39 130K danRer1_netBlastz.sql 2013-10-01 12:48 675 danRer1_netBlastz.txt.gz 2004-11-16 10:08 9.2M estOrientInfo.sql 2016-05-15 11:45 1.8K estOrientInfo.txt.gz 2016-05-15 11:45 16M extFile.sql 2013-10-01 12:48 445 extFile.txt.gz 2004-11-16 10:08 181 galGal2_netBlastz.sql 2013-10-01 12:48 675 galGal2_netBlastz.txt.gz 2004-11-16 10:08 3.4M gap.sql 2013-10-01 12:48 722 gap.txt.gz 2004-11-16 10:03 2.2M gbDelete_tmp.sql 2009-08-19 15:45 1.3K gbDelete_tmp.txt.gz 2009-08-19 15:45 157K gbLoaded.sql 2020-09-03 10:13 1.6K gbLoaded.txt.gz 2020-09-03 10:13 42K gc5Base.sql 2013-10-01 12:48 888 gc5Base.txt.gz 2004-11-16 10:08 6.8M genscan.sql 2013-10-01 12:48 748 genscan.txt.gz 2005-01-09 05:38 3.0M genscanPep.sql 2013-10-01 12:48 330 genscanPep.txt.gz 2004-11-16 10:09 11M gold.sql 2013-10-01 12:48 799 gold.txt.gz 2004-11-16 10:09 3.3M grp.sql 2014-03-02 04:18 1.4K grp.txt.gz 2014-03-02 04:18 223 hg17_netBlastz.sql 2013-10-01 12:48 669 hg17_netBlastz.txt.gz 2004-11-16 10:09 3.6M hgFindSpec.sql 2020-10-25 08:33 1.7K hgFindSpec.txt.gz 2020-10-25 08:33 666 history.sql 2010-07-04 19:18 1.6K history.txt.gz 2010-07-04 19:18 494 intronEst.sql 2016-05-15 11:44 2.1K intronEst.txt.gz 2016-05-15 11:44 32M jgiFilteredModels.sql 2013-10-01 12:48 768 jgiFilteredModels.txt.gz 2005-03-20 05:03 1.8M mgcFullMrna.sql 2020-03-01 09:23 2.1K mgcFullMrna.txt.gz 2020-03-01 09:23 957K mgcGenes.sql 2020-03-01 09:23 1.9K mgcGenes.txt.gz 2020-03-01 09:23 792K mm5_netBlastz.sql 2013-10-01 12:48 667 mm5_netBlastz.txt.gz 2004-11-16 10:09 3.6M mostConserved.sql 2013-10-01 12:48 650 mostConserved.txt.gz 2004-11-16 10:09 7.8M mrnaOrientInfo.sql 2020-05-11 17:36 1.8K mrnaOrientInfo.txt.gz 2020-05-11 17:36 380K multiz5way.sql 2013-10-01 12:48 661 multiz5way.txt.gz 2004-11-16 10:10 25M netDanRer1.sql 2013-10-01 12:48 1.3K netDanRer1.txt.gz 2004-11-16 10:10 24M netGalGal2.sql 2013-10-01 12:48 1.3K netGalGal2.txt.gz 2004-11-16 10:10 6.9M netHg18.sql 2013-10-01 12:48 1.3K netHg18.txt.gz 2006-04-15 06:38 5.9M netMm8.sql 2013-10-01 12:48 1.3K netMm8.txt.gz 2006-05-05 06:29 6.0M phastCons5.sql 2013-10-01 12:48 894 phastCons5.txt.gz 2004-11-16 10:11 14M rmsk.sql 2013-10-01 12:48 1.1K rmsk.txt.gz 2004-11-16 10:11 26M simpleRepeat.sql 2013-10-01 12:48 1.1K simpleRepeat.txt.gz 2004-11-16 10:12 15M tableDescriptions.sql 2019-07-21 03:43 1.4K tableDescriptions.txt.gz 2019-07-21 03:43 5.5K tableList.sql 2021-05-02 03:10 1.6K tableList.txt.gz 2021-05-02 03:10 3.3K trackDb.sql 2020-10-25 08:33 2.0K trackDb.txt.gz 2020-10-25 08:33 29K xenoRefFlat.sql 2020-09-03 10:13 1.7K xenoRefFlat.txt.gz 2020-09-03 10:13 32M xenoRefGene.sql 2020-09-03 10:13 1.9K xenoRefGene.txt.gz 2020-09-03 10:13 35M xenoRefSeqAli.sql 2020-09-03 10:13 2.1K xenoRefSeqAli.txt.gz 2020-09-03 10:13 34M