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 - bigFiles.txt.gz 2022-10-02 03:10 33 bigFiles.sql 2022-10-02 03:10 1.4K tableList.txt.gz 2022-10-02 03:10 3.3K tableList.sql 2022-10-02 03:10 1.6K hgFindSpec.txt.gz 2021-08-02 14:33 666 hgFindSpec.sql 2021-08-02 14:33 1.8K trackDb.txt.gz 2021-08-02 14:33 29K trackDb.sql 2021-08-02 14:33 2.1K xenoRefSeqAli.txt.gz 2020-09-03 10:13 34M xenoRefGene.txt.gz 2020-09-03 10:13 35M xenoRefFlat.txt.gz 2020-09-03 10:13 32M gbLoaded.txt.gz 2020-09-03 10:13 42K xenoRefSeqAli.sql 2020-09-03 10:13 2.1K xenoRefGene.sql 2020-09-03 10:13 1.9K xenoRefFlat.sql 2020-09-03 10:13 1.7K gbLoaded.sql 2020-09-03 10:13 1.6K mrnaOrientInfo.txt.gz 2020-05-11 17:36 380K all_mrna.txt.gz 2020-05-11 17:36 2.0M mrnaOrientInfo.sql 2020-05-11 17:36 1.8K all_mrna.sql 2020-05-11 17:36 2.1K mgcGenes.txt.gz 2020-03-01 09:23 792K mgcGenes.sql 2020-03-01 09:23 1.9K mgcFullMrna.txt.gz 2020-03-01 09:23 957K mgcFullMrna.sql 2020-03-01 09:23 2.1K tableDescriptions.txt.gz 2019-07-21 03:43 5.5K tableDescriptions.sql 2019-07-21 03:43 1.4K cytoBandIdeo.txt.gz 2018-05-13 08:39 130K cytoBandIdeo.sql 2018-05-13 08:39 1.5K estOrientInfo.txt.gz 2016-05-15 11:45 16M estOrientInfo.sql 2016-05-15 11:45 1.8K all_est.txt.gz 2016-05-15 11:45 57M all_est.sql 2016-05-15 11:45 2.1K intronEst.txt.gz 2016-05-15 11:44 32M intronEst.sql 2016-05-15 11:44 2.1K augustusGene.txt.gz 2015-07-26 17:28 2.4M augustusGene.sql 2015-07-26 17:28 1.9K cpgIslandExtUnmasked.txt.gz 2014-06-01 20:17 906K cpgIslandExtUnmasked.sql 2014-06-01 20:17 1.7K grp.txt.gz 2014-03-02 04:18 223 grp.sql 2014-03-02 04:18 1.4K simpleRepeat.sql 2013-10-01 12:48 1.1K rmsk.sql 2013-10-01 12:48 1.1K phastCons5.sql 2013-10-01 12:48 894 netMm8.sql 2013-10-01 12:48 1.3K netHg18.sql 2013-10-01 12:48 1.3K netGalGal2.sql 2013-10-01 12:48 1.3K netDanRer1.sql 2013-10-01 12:48 1.3K multiz5way.sql 2013-10-01 12:48 661 mostConserved.sql 2013-10-01 12:48 650 mm5_netBlastz.sql 2013-10-01 12:48 667 jgiFilteredModels.sql 2013-10-01 12:48 768 hg17_netBlastz.sql 2013-10-01 12:48 669 gold.sql 2013-10-01 12:48 799 genscanPep.sql 2013-10-01 12:48 330 genscan.sql 2013-10-01 12:48 748 gc5Base.sql 2013-10-01 12:48 888 gap.sql 2013-10-01 12:48 722 galGal2_netBlastz.sql 2013-10-01 12:48 675 extFile.sql 2013-10-01 12:48 445 danRer1_netBlastz.sql 2013-10-01 12:48 675 cpgIslandExt.sql 2013-10-01 12:48 751 chromInfo.sql 2013-10-01 12:48 396 chainMm8Link.sql 2013-10-01 12:48 577 chainMm8.sql 2013-10-01 12:48 812 chainHg18Link.sql 2013-10-01 12:48 579 chainHg18.sql 2013-10-01 12:48 880 chainGalGal2Link.sql 2013-10-01 12:48 585 chainGalGal2.sql 2013-10-01 12:48 886 chainDanRer1Link.sql 2013-10-01 12:48 585 chainDanRer1.sql 2013-10-01 12:48 886 blatFr1.sql 2013-10-01 12:48 1.3K blastHg17KG.sql 2013-10-01 12:48 1.3K history.txt.gz 2010-07-04 19:18 494 history.sql 2010-07-04 19:18 1.6K gbDelete_tmp.txt.gz 2009-08-19 15:45 157K gbDelete_tmp.sql 2009-08-19 15:45 1.3K chainMm8.txt.gz 2006-05-05 06:35 26M chainMm8Link.txt.gz 2006-05-05 06:32 216M netMm8.txt.gz 2006-05-05 06:29 6.0M chainHg18.txt.gz 2006-04-15 06:39 57M netHg18.txt.gz 2006-04-15 06:38 5.9M chainHg18Link.txt.gz 2006-04-15 06:36 253M jgiFilteredModels.txt.gz 2005-03-20 05:03 1.8M blastHg17KG.txt.gz 2005-03-05 05:28 3.2M genscan.txt.gz 2005-01-09 05:38 3.0M blatFr1.txt.gz 2004-11-18 12:20 43M simpleRepeat.txt.gz 2004-11-16 10:12 15M rmsk.txt.gz 2004-11-16 10:11 26M phastCons5.txt.gz 2004-11-16 10:11 14M netGalGal2.txt.gz 2004-11-16 10:10 6.9M netDanRer1.txt.gz 2004-11-16 10:10 24M multiz5way.txt.gz 2004-11-16 10:10 25M mostConserved.txt.gz 2004-11-16 10:09 7.8M mm5_netBlastz.txt.gz 2004-11-16 10:09 3.6M hg17_netBlastz.txt.gz 2004-11-16 10:09 3.6M gold.txt.gz 2004-11-16 10:09 3.3M genscanPep.txt.gz 2004-11-16 10:09 11M gc5Base.txt.gz 2004-11-16 10:08 6.8M galGal2_netBlastz.txt.gz 2004-11-16 10:08 3.4M extFile.txt.gz 2004-11-16 10:08 181 danRer1_netBlastz.txt.gz 2004-11-16 10:08 9.2M cpgIslandExt.txt.gz 2004-11-16 10:07 842K chromInfo.txt.gz 2004-11-16 10:07 131K gap.txt.gz 2004-11-16 10:03 2.2M chainGalGal2Link.txt.gz 2004-11-16 09:57 63M chainGalGal2.txt.gz 2004-11-16 09:56 11M chainDanRer1Link.txt.gz 2004-11-16 09:50 710M chainDanRer1.txt.gz 2004-11-16 09:43 169M