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 -
gap.sql 2006-06-13 07:13 1.5K
gap.txt.gz 2006-06-13 07:13 2.1M
chainRn4.sql 2006-06-13 07:13 1.6K
chainRn4.txt.gz 2006-06-13 07:14 44M
chainRn4Link.sql 2006-06-13 07:14 1.4K
chainRn4Link.txt.gz 2006-06-13 07:17 283M
chromInfo.sql 2006-06-13 07:20 1.2K
chromInfo.txt.gz 2006-06-13 07:20 100K
cpgIslandExt.sql 2006-06-13 07:20 1.6K
cpgIslandExt.txt.gz 2006-06-13 07:20 858K
gc5Base.sql 2006-06-13 07:21 1.7K
gc5Base.txt.gz 2006-06-13 07:21 6.4M
genscan.sql 2006-06-13 07:21 1.5K
genscan.txt.gz 2006-06-13 07:21 2.8M
genscanSubopt.sql 2006-06-13 07:21 1.4K
genscanSubopt.txt.gz 2006-06-13 07:21 4.6M
gold.sql 2006-06-13 07:21 1.6K
gold.txt.gz 2006-06-13 07:21 3.1M
netRn4.sql 2006-06-13 07:23 2.2K
netRn4.txt.gz 2006-06-13 07:23 7.0M
rmsk.sql 2006-06-13 07:23 1.8K
rmsk.txt.gz 2006-06-13 07:23 46M
simpleRepeat.sql 2006-06-13 07:24 1.9K
simpleRepeat.txt.gz 2006-06-13 07:24 15M
multiz7way.sql 2006-06-21 08:48 1.4K
multiz7way.txt.gz 2006-06-21 08:49 21M
multiz7wayFrames.sql 2006-06-21 08:49 1.5K
multiz7wayFrames.txt.gz 2006-06-21 08:49 6.0M
multiz7waySummary.sql 2006-06-21 08:49 1.4K
multiz7waySummary.txt.gz 2006-06-21 08:49 6.5M
phastCons7way.sql 2006-06-21 08:49 1.7K
phastCons7way.txt.gz 2006-06-21 08:50 14M
phastConsElements7way.sql 2006-06-21 08:50 1.4K
phastConsElements7way.txt.gz 2006-06-21 08:50 6.8M
microsat.sql 2006-08-03 07:52 1.3K
microsat.txt.gz 2006-08-03 07:52 139K
chainGalGal3.sql 2006-08-06 19:48 1.6K
chainGalGal3.txt.gz 2006-08-06 19:48 17M
chainGalGal3Link.sql 2006-08-06 19:49 1.4K
chainGalGal3Link.txt.gz 2006-08-06 19:49 79M
netGalGal3.sql 2006-08-06 19:50 2.2K
netGalGal3.txt.gz 2006-08-06 19:50 6.3M
chainMonDom4.sql 2006-08-11 12:18 1.6K
chainMonDom4.txt.gz 2006-08-11 12:21 219M
chainMonDom4Link.sql 2006-08-11 12:23 1.4K
chainMonDom4Link.txt.gz 2006-08-11 12:34 771M
netMonDom4.sql 2006-08-11 12:45 2.2K
netMonDom4.txt.gz 2006-08-11 12:45 7.0M
chainMm9Link.sql 2007-11-06 18:28 1.4K
chainMm9Link.txt.gz 2007-11-06 18:34 291M
netMm9.sql 2007-11-06 18:41 2.2K
netMm9.txt.gz 2007-11-06 18:41 8.8M
chainMm9.sql 2007-11-06 18:41 1.6K
chainMm9.txt.gz 2007-11-06 18:42 46M
chainHg19.sql 2009-10-04 12:58 1.8K
chainHg19.txt.gz 2009-10-04 12:58 126M
chainHg19Link.sql 2009-10-04 12:59 1.5K
chainHg19Link.txt.gz 2009-10-04 13:01 494M
netHg19.sql 2009-10-04 13:04 2.3K
netHg19.txt.gz 2009-10-04 13:04 9.3M
blastHg18KG.sql 2009-12-20 16:08 2.3K
blastHg18KG.txt.gz 2009-12-20 16:08 2.6M
history.sql 2010-07-04 19:18 1.6K
history.txt.gz 2010-07-04 19:18 732
ensGene.sql 2011-03-15 13:12 1.9K
ensGene.txt.gz 2011-03-15 13:12 2.0M
ensPep.sql 2011-03-15 13:13 1.3K
ensPep.txt.gz 2011-03-15 13:13 5.7M
ensGtp.sql 2011-03-15 13:14 1.4K
ensGtp.txt.gz 2011-03-15 13:14 235K
chainDanRer7Link.sql 2011-03-24 09:31 1.5K
chainDanRer7Link.txt.gz 2011-03-24 09:36 652M
chainDanRer7.sql 2011-03-24 09:49 1.6K
chainDanRer7.txt.gz 2011-03-24 09:51 224M
netDanRer7.sql 2011-03-24 09:55 2.0K
netDanRer7.txt.gz 2011-03-24 09:55 9.2M
chainAnoCar2.sql 2011-10-16 03:59 1.6K
chainAnoCar2.txt.gz 2011-10-16 04:00 51M
chainAnoCar2Link.sql 2011-10-16 04:00 1.5K
chainAnoCar2Link.txt.gz 2011-10-16 04:01 253M
netAnoCar2.sql 2011-10-16 04:03 2.0K
netAnoCar2.txt.gz 2011-10-16 04:03 9.6M
pubsBlatPsl.sql 2012-05-09 13:11 2.1K
pubsBlatPsl.txt.gz 2012-05-09 13:11 464K
pubsBlat.sql 2012-05-09 13:12 1.9K
pubsBlat.txt.gz 2012-05-09 13:12 315K
pubsBingBlat.sql 2014-01-26 19:44 2.4K
pubsBingBlat.txt.gz 2014-01-26 19:44 544K
pubsBingBlatPsl.sql 2014-01-26 19:44 2.2K
pubsBingBlatPsl.txt.gz 2014-01-26 19:44 461K
grp.sql 2014-03-02 04:18 1.4K
grp.txt.gz 2014-03-02 04:18 223
cpgIslandExtUnmasked.sql 2014-06-01 20:18 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 20:18 481K
extFile.sql 2014-10-19 15:46 1.5K
extFile.txt.gz 2014-10-19 15:46 85
augustusGene.sql 2015-07-26 17:28 1.9K
augustusGene.txt.gz 2015-07-26 17:28 2.4M
estOrientInfo.sql 2016-05-15 11:45 1.8K
estOrientInfo.txt.gz 2016-05-15 11:45 15M
intronEst.sql 2016-05-15 11:45 2.1K
intronEst.txt.gz 2016-05-15 11:45 32M
all_est.sql 2016-05-15 11:45 2.1K
all_est.txt.gz 2016-05-15 11:45 55M
mgcGenes.sql 2020-03-01 09:24 1.9K
mgcGenes.txt.gz 2020-03-01 09:24 788K
mgcFullMrna.sql 2020-03-01 09:24 2.1K
mgcFullMrna.txt.gz 2020-03-01 09:24 944K
all_mrna.sql 2020-05-11 17:36 2.1K
all_mrna.txt.gz 2020-05-11 17:36 1.9M
gbLoaded.sql 2020-09-03 10:13 1.6K
gbLoaded.txt.gz 2020-09-03 10:13 42K
mrnaOrientInfo.sql 2020-09-03 10:13 1.8K
mrnaOrientInfo.txt.gz 2020-09-03 10:13 528K
refFlat.sql 2020-09-03 10:13 1.7K
refFlat.txt.gz 2020-09-03 10:13 825K
refGene.sql 2020-09-03 10:13 1.9K
refGene.txt.gz 2020-09-03 10:13 901K
refSeqAli.sql 2020-09-03 10:13 2.1K
refSeqAli.txt.gz 2020-09-03 10:13 943K
xenoRefFlat.sql 2020-09-03 10:13 1.7K
xenoRefFlat.txt.gz 2020-09-03 10:13 23M
xenoRefGene.sql 2020-09-03 10:13 2.0K
xenoRefGene.txt.gz 2020-09-03 10:13 26M
xenoRefSeqAli.sql 2020-09-03 10:13 2.1K
xenoRefSeqAli.txt.gz 2020-09-03 10:13 24M
trackDb.sql 2023-03-28 13:54 2.1K
trackDb.txt.gz 2023-03-28 13:54 43K
hgFindSpec.sql 2023-03-28 13:54 1.8K
hgFindSpec.txt.gz 2023-03-28 13:54 889
tableDescriptions.sql 2024-11-16 02:04 1.4K
tableDescriptions.txt.gz 2024-11-16 02:04 7.0K
tableList.sql 2024-11-17 03:23 1.6K
tableList.txt.gz 2024-11-17 03:23 4.5K
bigFiles.sql 2024-11-17 03:23 1.4K
bigFiles.txt.gz 2024-11-17 03:23 33