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 -
gc5BaseBw.txt.gz 2011-11-02 17:56 63
bigFiles.txt.gz 2024-11-24 03:27 68
extFile.txt.gz 2011-11-02 17:29 79
grp.txt.gz 2014-03-02 04:18 208
hgFindSpec.txt.gz 2023-03-28 13:54 1.0K
history.txt.gz 2011-11-02 17:16 1.0K
gc5BaseBw.sql 2011-11-02 17:56 1.2K
ucscToEnsembl.sql 2011-11-02 17:56 1.3K
chromInfo.sql 2011-11-02 16:50 1.3K
ensPep.sql 2019-02-10 03:42 1.3K
grp.sql 2014-03-02 04:18 1.3K
extFile.sql 2011-11-02 17:29 1.4K
ensemblSource.sql 2019-02-10 03:42 1.4K
bigFiles.sql 2024-11-24 03:27 1.4K
ensemblToGeneName.sql 2019-02-10 03:42 1.4K
windowmaskerSdust.sql 2011-11-02 18:02 1.4K
microsat.sql 2011-11-02 17:05 1.4K
ensGtp.sql 2019-02-10 03:42 1.4K
chromAlias.sql 2018-08-05 09:41 1.4K
tableDescriptions.sql 2024-11-23 02:04 1.4K
multiz9way.sql 2011-12-11 14:37 1.5K
chainRn4Link.sql 2011-11-02 17:56 1.5K
ctgPos2.sql 2011-11-02 17:16 1.5K
chainHg19Link.sql 2011-11-02 17:06 1.5K
chainAnoCar2Link.sql 2011-11-02 16:52 1.5K
chainDanRer7Link.sql 2011-11-02 17:16 1.5K
chainGalGal3Link.sql 2011-11-02 17:33 1.5K
chainMelGal1Link.sql 2011-11-02 16:51 1.5K
chainMonDom5Link.sql 2011-11-02 17:41 1.5K
phastConsElements9way.sql 2011-12-11 14:36 1.5K
genscanSubopt.sql 2011-11-02 18:03 1.5K
history.sql 2011-11-02 17:16 1.5K
multiz9waySummary.sql 2011-12-11 14:37 1.5K
cytoBandIdeo.sql 2013-04-28 22:43 1.5K
gap.sql 2011-11-02 17:05 1.5K
chainMm10Link.sql 2013-10-27 22:20 1.5K
tableList.sql 2024-11-24 03:27 1.6K
gold.sql 2011-11-02 17:06 1.6K
gbLoaded.sql 2020-09-03 10:12 1.6K
genscan.sql 2011-11-02 17:15 1.6K
cpgIslandExt.sql 2011-11-02 16:50 1.6K
chainRn4.sql 2011-11-02 18:03 1.6K
chainHg19.sql 2011-11-02 17:54 1.6K
chainAnoCar2.sql 2011-11-02 17:53 1.6K
chainDanRer7.sql 2011-11-02 17:30 1.6K
chainGalGal3.sql 2011-11-02 17:54 1.6K
chainMelGal1.sql 2011-11-02 17:29 1.6K
chainMonDom5.sql 2011-11-02 18:00 1.6K
multiz9wayFrames.sql 2011-12-11 14:36 1.7K
tRNAs.sql 2012-04-16 05:38 1.7K
phyloP9way.sql 2011-12-11 14:36 1.7K
phastCons9way.sql 2011-12-11 14:36 1.7K
chainMm10.sql 2013-10-27 22:20 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 20:18 1.7K
refFlat.sql 2020-09-03 10:12 1.7K
hgFindSpec.sql 2023-03-28 13:54 1.8K
estOrientInfo.sql 2016-05-15 11:46 1.8K
rmsk.sql 2011-11-02 17:29 1.8K
mrnaOrientInfo.sql 2020-09-03 10:12 1.8K
simpleRepeat.sql 2011-11-02 16:50 1.9K
nestedRepeats.sql 2011-11-02 17:54 1.9K
ensGene.sql 2019-02-10 03:42 1.9K
mgcGenes.sql 2020-03-01 09:24 1.9K
augustusGene.sql 2015-07-26 17:28 1.9K
refGene.sql 2020-09-03 10:12 1.9K
netRn4.sql 2011-11-02 17:54 2.0K
netHg19.sql 2011-11-02 17:05 2.0K
netAnoCar2.sql 2011-11-02 17:53 2.0K
netDanRer7.sql 2011-11-02 17:34 2.0K
netGalGal3.sql 2011-11-02 17:54 2.0K
netMelGal1.sql 2011-11-02 17:16 2.0K
netMonDom5.sql 2011-11-02 18:02 2.0K
blastHg18KG.sql 2011-11-02 17:16 2.1K
trackDb.sql 2023-03-28 13:54 2.1K
netMm10.sql 2013-10-27 22:20 2.1K
all_est.sql 2016-05-15 11:46 2.1K
intronEst.sql 2016-05-15 11:46 2.1K
mgcFullMrna.sql 2020-03-01 09:24 2.1K
all_mrna.sql 2020-05-11 17:36 2.1K
refSeqAli.sql 2020-09-03 10:12 2.1K
tableList.txt.gz 2024-11-24 03:27 4.1K
tableDescriptions.txt.gz 2024-11-23 02:04 6.9K
trackDb.txt.gz 2023-03-28 13:54 39K
tRNAs.txt.gz 2012-04-16 05:38 56K
gbLoaded.txt.gz 2020-09-03 10:12 69K
ensemblSource.txt.gz 2019-02-10 03:42 73K
chromAlias.txt.gz 2018-08-05 09:41 92K
cytoBandIdeo.txt.gz 2013-04-28 22:43 93K
chromInfo.txt.gz 2011-11-02 16:50 94K
ucscToEnsembl.txt.gz 2011-11-02 17:56 97K
microsat.txt.gz 2011-11-02 17:05 136K
ensemblToGeneName.txt.gz 2019-02-10 03:42 140K
ctgPos2.txt.gz 2011-11-02 17:16 186K
ensGtp.txt.gz 2019-02-10 03:42 234K
cpgIslandExt.txt.gz 2011-11-02 16:50 316K
mrnaOrientInfo.txt.gz 2020-09-03 10:12 514K
mgcGenes.txt.gz 2020-03-01 09:24 764K
refFlat.txt.gz 2020-09-03 10:12 803K
cpgIslandExtUnmasked.txt.gz 2014-06-01 20:18 854K
refGene.txt.gz 2020-09-03 10:12 879K
refSeqAli.txt.gz 2020-09-03 10:12 942K
mgcFullMrna.txt.gz 2020-03-01 09:24 971K
all_mrna.txt.gz 2020-05-11 17:36 1.9M
gap.txt.gz 2011-11-02 17:05 2.0M
ensGene.txt.gz 2019-02-10 03:42 2.1M
augustusGene.txt.gz 2015-07-26 17:28 2.3M
genscan.txt.gz 2011-11-02 17:15 2.6M
blastHg18KG.txt.gz 2011-11-02 17:16 2.7M
gold.txt.gz 2011-11-02 17:06 2.8M
nestedRepeats.txt.gz 2011-11-02 17:54 2.9M
chainMelGal1.txt.gz 2011-11-02 17:29 4.0M
genscanSubopt.txt.gz 2011-11-02 18:03 4.3M
netMelGal1.txt.gz 2011-11-02 17:16 5.7M
multiz9waySummary.txt.gz 2011-12-11 14:37 6.1M
netGalGal3.txt.gz 2011-11-02 17:54 6.3M
ensPep.txt.gz 2019-02-10 03:42 6.6M
netRn4.txt.gz 2011-11-02 17:54 7.2M
netMonDom5.txt.gz 2011-11-02 18:02 7.3M
phastConsElements9way.txt.gz 2011-12-11 14:36 8.1M
netAnoCar2.txt.gz 2011-11-02 17:53 8.4M
netMm10.txt.gz 2013-10-27 22:20 9.2M
netHg19.txt.gz 2011-11-02 17:05 9.2M
netDanRer7.txt.gz 2011-11-02 17:34 9.7M
phastCons9way.txt.gz 2011-12-11 14:36 14M
phyloP9way.txt.gz 2011-12-11 14:36 14M
estOrientInfo.txt.gz 2016-05-15 11:46 14M
chainGalGal3.txt.gz 2011-11-02 17:54 17M
simpleRepeat.txt.gz 2011-11-02 16:50 19M
multiz9wayFrames.txt.gz 2011-12-11 14:36 20M
chainMelGal1Link.txt.gz 2011-11-02 16:52 26M
intronEst.txt.gz 2016-05-15 11:46 32M
multiz9way.txt.gz 2011-12-11 14:37 37M
rmsk.txt.gz 2011-11-02 17:29 43M
chainRn4.txt.gz 2011-11-02 18:03 44M
windowmaskerSdust.txt.gz 2011-11-02 18:03 45M
all_est.txt.gz 2016-05-15 11:46 53M
chainMm10.txt.gz 2013-10-27 22:20 55M
chainAnoCar2.txt.gz 2011-11-02 17:53 64M
chainGalGal3Link.txt.gz 2011-11-02 17:33 79M
chainHg19.txt.gz 2011-11-02 17:55 124M
chainMonDom5.txt.gz 2011-11-02 18:01 218M
chainDanRer7.txt.gz 2011-11-02 17:31 223M
chainRn4Link.txt.gz 2011-11-02 17:57 285M
chainMm10Link.txt.gz 2013-10-27 22:21 370M
chainHg19Link.txt.gz 2011-11-02 17:08 482M
chainDanRer7Link.txt.gz 2011-11-02 17:19 665M
chainAnoCar2Link.txt.gz 2011-11-02 16:56 685M
chainMonDom5Link.txt.gz 2011-11-02 17:44 769M