This directory contains a dump of the UCSC genome annotation database for
the Nov. 2009 (JGI 4.2/xenTro3) assembly of the
Xenopus (Silurana) tropicalis (western clawed frog) genome
(xenTro3, US DOE Joint Genome Institute (JGI-PGF)
(GCA_000004195.1)) from the X. tropicalis Genome Consortium.
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the US DOE Joint Genome Institute (JGI).
For more information on the X. tropicalis genome, please note the
NCBI WGS Traces information:
http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAMC01
and the project website:
http://genome.jgi-psf.org/Xentr4/Xentr4.home.html
Files included in this directory (updated nightly):
- *.sql files: the MySQL commands used to create the tables
- *.txt.gz files: the database tables in a tab-delimited format
compressed with gzip.
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=xenTro3
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
---------------------------------------------------------------
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/xenTro3/database/. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Alternate methods to ftp access.
Using an rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/database/gc5BaseBw.txt.gz'
-O gc5BaseBw.txt.gz
Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.cse.ucsc.edu/gbdb/
To uncompress the *.txt.gz files:
gunzip <table>.txt.gz
The tables can be loaded directly from the .txt.gz compressed file.
It is not necessary to uncompress them to load into a database,
as shown in the example below.
To load one of the tables directly into your local mirror database,
for example the table chromInfo:
## create table from the sql definition
$ hgsql xenTro3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql xenTro3 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
==========================================================================
Data use policy from:
http://genome.jgi-psf.org/Xentr4/Xentr4.download.html
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 -
windowmaskerSdust.txt.gz 2011-11-02 18:03 45M
windowmaskerSdust.sql 2011-11-02 18:02 1.4K
ucscToEnsembl.txt.gz 2011-11-02 17:56 97K
ucscToEnsembl.sql 2011-11-02 17:56 1.3K
trackDb.txt.gz 2023-03-28 13:54 39K
trackDb.sql 2023-03-28 13:54 2.1K
tableList.txt.gz 2024-11-24 03:27 4.1K
tableList.sql 2024-11-24 03:27 1.6K
tableDescriptions.txt.gz 2024-11-23 02:04 6.9K
tableDescriptions.sql 2024-11-23 02:04 1.4K
tRNAs.txt.gz 2012-04-16 05:38 56K
tRNAs.sql 2012-04-16 05:38 1.7K
simpleRepeat.txt.gz 2011-11-02 16:50 19M
simpleRepeat.sql 2011-11-02 16:50 1.9K
rmsk.txt.gz 2011-11-02 17:29 43M
rmsk.sql 2011-11-02 17:29 1.8K
refSeqAli.txt.gz 2020-09-03 10:12 942K
refSeqAli.sql 2020-09-03 10:12 2.1K
refGene.txt.gz 2020-09-03 10:12 879K
refGene.sql 2020-09-03 10:12 1.9K
refFlat.txt.gz 2020-09-03 10:12 803K
refFlat.sql 2020-09-03 10:12 1.7K
phyloP9way.txt.gz 2011-12-11 14:36 14M
phyloP9way.sql 2011-12-11 14:36 1.7K
phastConsElements9way.txt.gz 2011-12-11 14:36 8.1M
phastConsElements9way.sql 2011-12-11 14:36 1.5K
phastCons9way.txt.gz 2011-12-11 14:36 14M
phastCons9way.sql 2011-12-11 14:36 1.7K
netRn4.txt.gz 2011-11-02 17:54 7.2M
netRn4.sql 2011-11-02 17:54 2.0K
netMonDom5.txt.gz 2011-11-02 18:02 7.3M
netMonDom5.sql 2011-11-02 18:02 2.0K
netMm10.txt.gz 2013-10-27 22:20 9.2M
netMm10.sql 2013-10-27 22:20 2.1K
netMelGal1.txt.gz 2011-11-02 17:16 5.7M
netMelGal1.sql 2011-11-02 17:16 2.0K
netHg19.txt.gz 2011-11-02 17:05 9.2M
netHg19.sql 2011-11-02 17:05 2.0K
netGalGal3.txt.gz 2011-11-02 17:54 6.3M
netGalGal3.sql 2011-11-02 17:54 2.0K
netDanRer7.txt.gz 2011-11-02 17:34 9.7M
netDanRer7.sql 2011-11-02 17:34 2.0K
netAnoCar2.txt.gz 2011-11-02 17:53 8.4M
netAnoCar2.sql 2011-11-02 17:53 2.0K
nestedRepeats.txt.gz 2011-11-02 17:54 2.9M
nestedRepeats.sql 2011-11-02 17:54 1.9K
multiz9waySummary.txt.gz 2011-12-11 14:37 6.1M
multiz9waySummary.sql 2011-12-11 14:37 1.5K
multiz9wayFrames.txt.gz 2011-12-11 14:36 20M
multiz9wayFrames.sql 2011-12-11 14:36 1.7K
multiz9way.txt.gz 2011-12-11 14:37 37M
multiz9way.sql 2011-12-11 14:37 1.5K
mrnaOrientInfo.txt.gz 2020-09-03 10:12 514K
mrnaOrientInfo.sql 2020-09-03 10:12 1.8K
microsat.txt.gz 2011-11-02 17:05 136K
microsat.sql 2011-11-02 17:05 1.4K
mgcGenes.txt.gz 2020-03-01 09:24 764K
mgcGenes.sql 2020-03-01 09:24 1.9K
mgcFullMrna.txt.gz 2020-03-01 09:24 971K
mgcFullMrna.sql 2020-03-01 09:24 2.1K
intronEst.txt.gz 2016-05-15 11:46 32M
intronEst.sql 2016-05-15 11:46 2.1K
history.txt.gz 2011-11-02 17:16 1.0K
history.sql 2011-11-02 17:16 1.5K
hgFindSpec.txt.gz 2023-03-28 13:54 1.0K
hgFindSpec.sql 2023-03-28 13:54 1.8K
grp.txt.gz 2014-03-02 04:18 208
grp.sql 2014-03-02 04:18 1.3K
gold.txt.gz 2011-11-02 17:06 2.8M
gold.sql 2011-11-02 17:06 1.6K
genscanSubopt.txt.gz 2011-11-02 18:03 4.3M
genscanSubopt.sql 2011-11-02 18:03 1.5K
genscan.txt.gz 2011-11-02 17:15 2.6M
genscan.sql 2011-11-02 17:15 1.6K
gc5BaseBw.txt.gz 2011-11-02 17:56 63
gc5BaseBw.sql 2011-11-02 17:56 1.2K
gbLoaded.txt.gz 2020-09-03 10:12 69K
gbLoaded.sql 2020-09-03 10:12 1.6K
gap.txt.gz 2011-11-02 17:05 2.0M
gap.sql 2011-11-02 17:05 1.5K
extFile.txt.gz 2011-11-02 17:29 79
extFile.sql 2011-11-02 17:29 1.4K
estOrientInfo.txt.gz 2016-05-15 11:46 14M
estOrientInfo.sql 2016-05-15 11:46 1.8K
ensemblToGeneName.txt.gz 2019-02-10 03:42 140K
ensemblToGeneName.sql 2019-02-10 03:42 1.4K
ensemblSource.txt.gz 2019-02-10 03:42 73K
ensemblSource.sql 2019-02-10 03:42 1.4K
ensPep.txt.gz 2019-02-10 03:42 6.6M
ensPep.sql 2019-02-10 03:42 1.3K
ensGtp.txt.gz 2019-02-10 03:42 234K
ensGtp.sql 2019-02-10 03:42 1.4K
ensGene.txt.gz 2019-02-10 03:42 2.1M
ensGene.sql 2019-02-10 03:42 1.9K
cytoBandIdeo.txt.gz 2013-04-28 22:43 93K
cytoBandIdeo.sql 2013-04-28 22:43 1.5K
ctgPos2.txt.gz 2011-11-02 17:16 186K
ctgPos2.sql 2011-11-02 17:16 1.5K
cpgIslandExtUnmasked.txt.gz 2014-06-01 20:18 854K
cpgIslandExtUnmasked.sql 2014-06-01 20:18 1.7K
cpgIslandExt.txt.gz 2011-11-02 16:50 316K
cpgIslandExt.sql 2011-11-02 16:50 1.6K
chromInfo.txt.gz 2011-11-02 16:50 94K
chromInfo.sql 2011-11-02 16:50 1.3K
chromAlias.txt.gz 2018-08-05 09:41 92K
chromAlias.sql 2018-08-05 09:41 1.4K
chainRn4Link.txt.gz 2011-11-02 17:57 285M
chainRn4Link.sql 2011-11-02 17:56 1.5K
chainRn4.txt.gz 2011-11-02 18:03 44M
chainRn4.sql 2011-11-02 18:03 1.6K
chainMonDom5Link.txt.gz 2011-11-02 17:44 769M
chainMonDom5Link.sql 2011-11-02 17:41 1.5K
chainMonDom5.txt.gz 2011-11-02 18:01 218M
chainMonDom5.sql 2011-11-02 18:00 1.6K
chainMm10Link.txt.gz 2013-10-27 22:21 370M
chainMm10Link.sql 2013-10-27 22:20 1.5K
chainMm10.txt.gz 2013-10-27 22:20 55M
chainMm10.sql 2013-10-27 22:20 1.7K
chainMelGal1Link.txt.gz 2011-11-02 16:52 26M
chainMelGal1Link.sql 2011-11-02 16:51 1.5K
chainMelGal1.txt.gz 2011-11-02 17:29 4.0M
chainMelGal1.sql 2011-11-02 17:29 1.6K
chainHg19Link.txt.gz 2011-11-02 17:08 482M
chainHg19Link.sql 2011-11-02 17:06 1.5K
chainHg19.txt.gz 2011-11-02 17:55 124M
chainHg19.sql 2011-11-02 17:54 1.6K
chainGalGal3Link.txt.gz 2011-11-02 17:33 79M
chainGalGal3Link.sql 2011-11-02 17:33 1.5K
chainGalGal3.txt.gz 2011-11-02 17:54 17M
chainGalGal3.sql 2011-11-02 17:54 1.6K
chainDanRer7Link.txt.gz 2011-11-02 17:19 665M
chainDanRer7Link.sql 2011-11-02 17:16 1.5K
chainDanRer7.txt.gz 2011-11-02 17:31 223M
chainDanRer7.sql 2011-11-02 17:30 1.6K
chainAnoCar2Link.txt.gz 2011-11-02 16:56 685M
chainAnoCar2Link.sql 2011-11-02 16:52 1.5K
chainAnoCar2.txt.gz 2011-11-02 17:53 64M
chainAnoCar2.sql 2011-11-02 17:53 1.6K
blastHg18KG.txt.gz 2011-11-02 17:16 2.7M
blastHg18KG.sql 2011-11-02 17:16 2.1K
bigFiles.txt.gz 2024-11-24 03:27 68
bigFiles.sql 2024-11-24 03:27 1.4K
augustusGene.txt.gz 2015-07-26 17:28 2.3M
augustusGene.sql 2015-07-26 17:28 1.9K
all_mrna.txt.gz 2020-05-11 17:36 1.9M
all_mrna.sql 2020-05-11 17:36 2.1K
all_est.txt.gz 2016-05-15 11:46 53M
all_est.sql 2016-05-15 11:46 2.1K