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 2024-12-29 03:26 33
extFile.txt.gz 2004-11-16 10:08 181
grp.txt.gz 2014-03-02 04:18 223
genscanPep.sql 2013-10-01 12:48 330
chromInfo.sql 2013-10-01 12:48 396
extFile.sql 2013-10-01 12:48 445
history.txt.gz 2010-07-04 19:18 494
chainMm8Link.sql 2013-10-01 12:48 577
chainHg18Link.sql 2013-10-01 12:48 579
chainDanRer1Link.sql 2013-10-01 12:48 585
chainGalGal2Link.sql 2013-10-01 12:48 585
mostConserved.sql 2013-10-01 12:48 650
multiz5way.sql 2013-10-01 12:48 661
mm5_netBlastz.sql 2013-10-01 12:48 667
hg17_netBlastz.sql 2013-10-01 12:48 669
danRer1_netBlastz.sql 2013-10-01 12:48 675
galGal2_netBlastz.sql 2013-10-01 12:48 675
hgFindSpec.txt.gz 2023-03-28 13:54 712
gap.sql 2013-10-01 12:48 722
genscan.sql 2013-10-01 12:48 748
cpgIslandExt.sql 2013-10-01 12:48 751
jgiFilteredModels.sql 2013-10-01 12:48 768
gold.sql 2013-10-01 12:48 799
chainMm8.sql 2013-10-01 12:48 812
chainHg18.sql 2013-10-01 12:48 880
chainDanRer1.sql 2013-10-01 12:48 886
chainGalGal2.sql 2013-10-01 12:48 886
gc5Base.sql 2013-10-01 12:48 888
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
gbDelete_tmp.sql 2009-08-19 15:45 1.3K
blatFr1.sql 2013-10-01 12:48 1.3K
netMm8.sql 2013-10-01 12:48 1.3K
netHg18.sql 2013-10-01 12:48 1.3K
netDanRer1.sql 2013-10-01 12:48 1.3K
netGalGal2.sql 2013-10-01 12:48 1.3K
blastHg17KG.sql 2013-10-01 12:48 1.3K
grp.sql 2014-03-02 04:18 1.4K
bigFiles.sql 2024-12-29 03:26 1.4K
tableDescriptions.sql 2024-12-28 02:12 1.5K
cytoBandIdeo.sql 2018-05-13 08:39 1.5K
history.sql 2010-07-04 19:18 1.6K
tableList.sql 2024-12-29 03:26 1.6K
gbLoaded.sql 2020-09-03 10:13 1.6K
cpgIslandExtUnmasked.sql 2014-06-01 20:17 1.7K
xenoRefFlat.sql 2020-09-03 10:13 1.7K
hgFindSpec.sql 2023-03-28 13:54 1.8K
estOrientInfo.sql 2016-05-15 11:45 1.8K
mrnaOrientInfo.sql 2020-05-11 17:36 1.8K
mgcGenes.sql 2020-03-01 09:23 1.9K
augustusGene.sql 2015-07-26 17:28 1.9K
xenoRefGene.sql 2020-09-03 10:13 2.0K
trackDb.sql 2023-03-28 13:54 2.1K
all_est.sql 2016-05-15 11:45 2.1K
intronEst.sql 2016-05-15 11:44 2.1K
mgcFullMrna.sql 2020-03-01 09:23 2.1K
all_mrna.sql 2020-05-11 17:36 2.1K
xenoRefSeqAli.sql 2020-09-03 10:13 2.1K
tableList.txt.gz 2024-12-29 03:26 3.3K
tableDescriptions.txt.gz 2024-12-28 02:12 5.6K
trackDb.txt.gz 2023-03-28 13:54 30K
gbLoaded.txt.gz 2020-09-03 10:13 42K
cytoBandIdeo.txt.gz 2018-05-13 08:39 130K
chromInfo.txt.gz 2004-11-16 10:07 131K
gbDelete_tmp.txt.gz 2009-08-19 15:45 157K
mrnaOrientInfo.txt.gz 2020-05-11 17:36 380K
mgcGenes.txt.gz 2020-03-01 09:23 792K
cpgIslandExt.txt.gz 2004-11-16 10:07 842K
cpgIslandExtUnmasked.txt.gz 2014-06-01 20:17 906K
mgcFullMrna.txt.gz 2020-03-01 09:23 957K
jgiFilteredModels.txt.gz 2005-03-20 05:03 1.8M
all_mrna.txt.gz 2020-05-11 17:36 2.0M
gap.txt.gz 2004-11-16 10:03 2.2M
augustusGene.txt.gz 2015-07-26 17:28 2.4M
genscan.txt.gz 2005-01-09 05:38 3.0M
blastHg17KG.txt.gz 2005-03-05 05:28 3.2M
gold.txt.gz 2004-11-16 10:09 3.3M
galGal2_netBlastz.txt.gz 2004-11-16 10:08 3.4M
mm5_netBlastz.txt.gz 2004-11-16 10:09 3.6M
hg17_netBlastz.txt.gz 2004-11-16 10:09 3.6M
netHg18.txt.gz 2006-04-15 06:38 5.9M
netMm8.txt.gz 2006-05-05 06:29 6.0M
gc5Base.txt.gz 2004-11-16 10:08 6.8M
netGalGal2.txt.gz 2004-11-16 10:10 6.9M
mostConserved.txt.gz 2004-11-16 10:09 7.8M
danRer1_netBlastz.txt.gz 2004-11-16 10:08 9.2M
chainGalGal2.txt.gz 2004-11-16 09:56 11M
genscanPep.txt.gz 2004-11-16 10:09 11M
phastCons5.txt.gz 2004-11-16 10:11 14M
simpleRepeat.txt.gz 2004-11-16 10:12 15M
estOrientInfo.txt.gz 2016-05-15 11:45 16M
netDanRer1.txt.gz 2004-11-16 10:10 24M
multiz5way.txt.gz 2004-11-16 10:10 25M
rmsk.txt.gz 2004-11-16 10:11 26M
chainMm8.txt.gz 2006-05-05 06:35 26M
xenoRefFlat.txt.gz 2020-09-03 10:13 32M
intronEst.txt.gz 2016-05-15 11:44 32M
xenoRefSeqAli.txt.gz 2020-09-03 10:13 34M
xenoRefGene.txt.gz 2020-09-03 10:13 35M
blatFr1.txt.gz 2004-11-18 12:20 43M
chainHg18.txt.gz 2006-04-15 06:39 57M
all_est.txt.gz 2016-05-15 11:45 57M
chainGalGal2Link.txt.gz 2004-11-16 09:57 63M
chainDanRer1.txt.gz 2004-11-16 09:43 169M
chainMm8Link.txt.gz 2006-05-05 06:32 216M
chainHg18Link.txt.gz 2006-04-15 06:36 253M
chainDanRer1Link.txt.gz 2004-11-16 09:50 710M