This directory contains a dump of the UCSC genome annotation database for
the Oct. 2011 (FUGU5/fr3) assembly of the fugu genome
(fr3, Fugu Genome Sequencing Consortium - FUGU5
(NCBI project 1434, GCA_000180615.2)).
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the Fugu Genome Sequencing Consortium,
http://www.fugu-sg.org/
as part of the International Fugu Genome Consortium, led by JGI and the
Singapore Institute of Molecular and Cell Biology (IMCB).
For more information on the fugu genome, see the project website:
http://www.fugu-sg.org/
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=fr3
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/fr3/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/fr3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/fr3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/fr3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/fr3/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 fr3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql fr3 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
==============================================================================
All the files and tables in this directory are freely usable for any purpose.
1. These data have been freely provided by the JGI for use in the
UCSC Genome Browser.
==============================================================================
Name Last modified Size Description
Parent Directory -
xenoMrna.txt.gz 2020-08-19 09:10 192M
xenoMrna.sql 2020-08-19 09:10 2.1K
windowmaskerSdust.txt.gz 2012-05-13 21:04 15M
windowmaskerSdust.sql 2012-05-13 21:04 1.4K
ucscToRefSeq.txt.gz 2018-02-18 06:31 52K
ucscToRefSeq.sql 2018-02-18 06:31 1.4K
ucscToINSDC.txt.gz 2019-02-10 03:41 50K
ucscToINSDC.sql 2019-02-10 03:41 1.4K
trackDb_pushedout.txt.gz 2023-12-05 13:51 43K
trackDb_pushedout.sql 2023-12-05 13:51 2.1K
trackDb.txt.gz 2023-12-05 13:51 43K
trackDb.sql 2023-12-05 13:51 2.1K
tableList.txt.gz 2024-04-14 03:33 4.9K
tableList.sql 2024-04-14 03:33 1.6K
tableDescriptions.txt.gz 2024-04-13 02:03 7.6K
tableDescriptions.sql 2024-04-13 02:03 1.5K
simpleRepeat.txt.gz 2012-05-13 20:53 3.4M
simpleRepeat.sql 2012-05-13 20:53 1.9K
seqNcbiRefSeq.txt.gz 2018-02-09 14:05 505K
seqNcbiRefSeq.sql 2018-02-09 14:05 1.6K
rmsk.txt.gz 2012-05-13 21:07 4.7M
rmsk.sql 2012-05-13 21:07 1.8K
refSeqAli.txt.gz 2020-08-19 09:23 49K
refSeqAli.sql 2020-08-19 09:23 2.1K
refGene.txt.gz 2020-08-19 09:22 47K
refGene.sql 2020-08-19 09:22 1.9K
refFlat.txt.gz 2020-08-19 09:22 42K
refFlat.sql 2020-08-19 09:22 1.7K
phyloP8way.txt.gz 2012-05-13 20:47 11M
phyloP8way.sql 2012-05-13 20:47 1.7K
phastConsElements8way.txt.gz 2012-05-13 21:07 11M
phastConsElements8way.sql 2012-05-13 21:07 1.5K
phastCons8way.txt.gz 2012-05-13 20:49 9.6M
phastCons8way.sql 2012-05-13 20:49 1.7K
netXenTro9.txt.gz 2017-12-14 10:21 4.9M
netXenTro9.sql 2017-12-14 10:21 2.1K
netTetNig2.txt.gz 2012-05-13 20:51 17M
netTetNig2.sql 2012-05-13 20:50 2.0K
netOryLat2.txt.gz 2012-05-13 21:05 12M
netOryLat2.sql 2012-05-13 21:05 2.0K
netOreNil1.txt.gz 2012-05-13 21:01 11M
netOreNil1.sql 2012-05-13 21:01 2.0K
netMm10.txt.gz 2013-08-04 13:04 4.8M
netMm10.sql 2013-08-04 13:04 2.1K
netLatCha1.txt.gz 2012-05-13 20:49 5.8M
netLatCha1.sql 2012-05-13 20:49 2.0K
netGasAcu1.txt.gz 2012-05-13 20:53 13M
netGasAcu1.sql 2012-05-13 20:53 2.0K
netGalGal6.txt.gz 2019-01-20 08:23 5.0M
netGalGal6.sql 2019-01-20 08:23 2.1K
netGadMor1.txt.gz 2012-05-13 21:04 9.8M
netGadMor1.sql 2012-05-13 21:04 2.0K
netDanRer7.txt.gz 2012-05-13 20:53 8.3M
netDanRer7.sql 2012-05-13 20:53 2.0K
nestedRepeats.txt.gz 2012-05-13 20:51 298K
nestedRepeats.sql 2012-05-13 20:51 1.9K
ncbiRefSeqPsl.txt.gz 2018-02-09 13:38 2.9M
ncbiRefSeqPsl.sql 2018-02-09 13:38 2.1K
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:38 2.4M
ncbiRefSeqPredicted.sql 2018-02-09 13:38 2.0K
ncbiRefSeqPepTable.txt.gz 2018-02-09 14:05 7.9M
ncbiRefSeqPepTable.sql 2018-02-09 14:05 1.4K
ncbiRefSeqOther.txt.gz 2018-02-09 14:05 71
ncbiRefSeqOther.sql 2018-02-09 14:05 1.3K
ncbiRefSeqLink.txt.gz 2018-02-09 13:38 1.0M
ncbiRefSeqLink.sql 2018-02-09 13:38 2.0K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:38 42K
ncbiRefSeqCurated.sql 2018-02-09 13:38 2.0K
ncbiRefSeqCds.txt.gz 2018-02-09 14:05 208K
ncbiRefSeqCds.sql 2018-02-09 14:05 1.4K
ncbiRefSeq.txt.gz 2018-02-09 13:38 2.4M
ncbiRefSeq.sql 2018-02-09 13:38 1.9K
multiz8waySummary.txt.gz 2012-05-13 21:07 2.3M
multiz8waySummary.sql 2012-05-13 21:07 1.5K
multiz8wayFrames.txt.gz 2012-05-13 20:55 14M
multiz8wayFrames.sql 2012-05-13 20:55 1.7K
multiz8way.txt.gz 2012-05-13 20:58 37M
multiz8way.sql 2012-05-13 20:58 1.5K
mrnaOrientInfo.txt.gz 2020-08-19 09:22 27K
mrnaOrientInfo.sql 2020-08-19 09:22 1.8K
microsat.txt.gz 2015-08-23 16:39 158K
microsat.sql 2015-08-23 16:39 1.5K
intronEst.txt.gz 2019-03-17 09:26 7.8M
intronEst.sql 2019-03-17 09:26 2.1K
history.txt.gz 2012-05-13 20:51 1.0K
history.sql 2012-05-13 20:51 1.5K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:51 1.2K
hgFindSpec_pushedout.sql 2023-12-05 13:51 1.8K
hgFindSpec.txt.gz 2023-12-05 13:51 1.2K
hgFindSpec.sql 2023-12-05 13:51 1.8K
grp.txt.gz 2014-03-02 03:40 208
grp.sql 2014-03-02 03:40 1.3K
gold.txt.gz 2012-05-13 20:47 268K
gold.sql 2012-05-13 20:47 1.6K
genscan.txt.gz 2013-12-09 23:13 1.3M
genscan.sql 2013-12-09 23:13 1.7K
gc5BaseBw.txt.gz 2012-05-13 20:59 59
gc5BaseBw.sql 2012-05-13 20:59 1.2K
gbLoaded.txt.gz 2020-08-19 09:27 41K
gbLoaded.sql 2020-08-19 09:27 1.6K
gap.txt.gz 2012-05-13 21:05 423K
gap.sql 2012-05-13 21:05 1.5K
extNcbiRefSeq.txt.gz 2018-02-09 14:05 86
extNcbiRefSeq.sql 2018-02-09 14:05 1.5K
extFile.txt.gz 2012-05-13 21:05 75
extFile.sql 2012-05-13 21:05 1.3K
estOrientInfo.txt.gz 2019-03-17 09:27 3.1M
estOrientInfo.sql 2019-03-17 09:27 1.8K
ensemblToGeneName.txt.gz 2019-02-10 03:41 164K
ensemblToGeneName.sql 2019-02-10 03:41 1.4K
ensemblSource.txt.gz 2019-02-10 03:41 80K
ensemblSource.sql 2019-02-10 03:41 1.3K
ensPep.txt.gz 2019-02-10 03:41 7.3M
ensPep.sql 2019-02-10 03:41 1.3K
ensGtp.txt.gz 2019-02-10 03:41 295K
ensGtp.sql 2019-02-10 03:41 1.4K
ensGene.txt.gz 2019-02-10 03:41 2.1M
ensGene.sql 2019-02-10 03:41 1.9K
cytoBandIdeo.txt.gz 2013-04-28 15:14 33K
cytoBandIdeo.sql 2013-04-28 15:14 1.5K
cpgIslandExtUnmasked.txt.gz 2019-04-14 03:21 1.0M
cpgIslandExtUnmasked.sql 2019-04-14 03:21 1.7K
cpgIslandExt.txt.gz 2019-04-14 03:21 726K
cpgIslandExt.sql 2019-04-14 03:21 1.7K
chromInfo.txt.gz 2012-05-13 20:55 33K
chromInfo.sql 2012-05-13 20:55 1.3K
chromAlias.txt.gz 2019-02-10 03:41 66K
chromAlias.sql 2019-02-10 03:41 1.4K
chainXenTro9Link.txt.gz 2017-12-14 10:20 47M
chainXenTro9Link.sql 2017-12-14 10:20 1.5K
chainXenTro9.txt.gz 2017-12-14 10:20 12M
chainXenTro9.sql 2017-12-14 10:20 1.7K
chainTetNig2Link.txt.gz 2012-05-13 20:58 106M
chainTetNig2Link.sql 2012-05-13 20:57 1.5K
chainTetNig2.txt.gz 2012-05-13 21:04 12M
chainTetNig2.sql 2012-05-13 21:04 1.6K
chainOryLat2Link.txt.gz 2012-05-13 20:56 185M
chainOryLat2Link.sql 2012-05-13 20:55 1.5K
chainOryLat2.txt.gz 2012-05-13 20:49 32M
chainOryLat2.sql 2012-05-13 20:49 1.6K
chainOreNil1Link.txt.gz 2012-05-13 21:02 189M
chainOreNil1Link.sql 2012-05-13 21:01 1.5K
chainOreNil1.txt.gz 2012-05-13 20:47 31M
chainOreNil1.sql 2012-05-13 20:47 1.6K
chainMm10Link.txt.gz 2013-08-04 13:03 31M
chainMm10Link.sql 2013-08-04 13:03 1.5K
chainMm10.txt.gz 2013-08-04 13:03 4.7M
chainMm10.sql 2013-08-04 13:03 1.7K
chainLatCha1Link.txt.gz 2012-05-13 21:05 41M
chainLatCha1Link.sql 2012-05-13 21:05 1.5K
chainLatCha1.txt.gz 2012-05-13 21:04 10M
chainLatCha1.sql 2012-05-13 21:04 1.6K
chainGasAcu1Link.txt.gz 2012-05-13 20:53 182M
chainGasAcu1Link.sql 2012-05-13 20:53 1.5K
chainGasAcu1.txt.gz 2012-05-13 21:06 29M
chainGasAcu1.sql 2012-05-13 21:06 1.6K
chainGalGal6Link.txt.gz 2019-01-20 08:23 30M
chainGalGal6Link.sql 2019-01-20 08:23 1.5K
chainGalGal6.txt.gz 2019-01-20 08:23 5.2M
chainGalGal6.sql 2019-01-20 08:23 1.7K
chainGadMor1Link.txt.gz 2012-05-13 20:52 92M
chainGadMor1Link.sql 2012-05-13 20:52 1.5K
chainGadMor1.txt.gz 2012-05-13 20:47 21M
chainGadMor1.sql 2012-05-13 20:47 1.6K
chainDanRer7Link.txt.gz 2012-05-13 21:05 109M
chainDanRer7Link.sql 2012-05-13 21:05 1.5K
chainDanRer7.txt.gz 2012-05-13 21:06 28M
chainDanRer7.sql 2012-05-13 21:06 1.6K
bigFiles.txt.gz 2024-04-14 03:33 90
bigFiles.sql 2024-04-14 03:33 1.4K
augustusGene.txt.gz 2015-07-26 13:38 2.4M
augustusGene.sql 2015-07-26 13:38 1.9K
all_mrna.txt.gz 2020-05-06 13:45 75K
all_mrna.sql 2020-05-06 13:45 2.1K
all_est.txt.gz 2019-03-17 09:27 13M
all_est.sql 2019-03-17 09:27 2.1K