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