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 -
gc5BaseBw.txt.gz 2012-05-13 20:59 59
ncbiRefSeqOther.txt.gz 2018-02-09 14:05 71
extFile.txt.gz 2012-05-13 21:05 75
extNcbiRefSeq.txt.gz 2018-02-09 14:05 86
bigFiles.txt.gz 2024-11-17 03:36 90
grp.txt.gz 2014-03-02 03:40 208
history.txt.gz 2012-05-13 20:51 1.0K
gc5BaseBw.sql 2012-05-13 20:59 1.2K
hgFindSpec.txt.gz 2023-12-05 13:51 1.2K
chromInfo.sql 2012-05-13 20:55 1.3K
ncbiRefSeqOther.sql 2018-02-09 14:05 1.3K
ensPep.sql 2019-02-10 03:41 1.3K
grp.sql 2014-03-02 03:40 1.3K
extFile.sql 2012-05-13 21:05 1.3K
ensemblSource.sql 2019-02-10 03:41 1.3K
ncbiRefSeqCds.sql 2018-02-09 14:05 1.4K
bigFiles.sql 2024-11-17 03:36 1.4K
ncbiRefSeqPepTable.sql 2018-02-09 14:05 1.4K
ensemblToGeneName.sql 2019-02-10 03:41 1.4K
ensGtp.sql 2019-02-10 03:41 1.4K
chromAlias.sql 2019-02-10 03:41 1.4K
ucscToINSDC.sql 2019-02-10 03:41 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.4K
ucscToRefSeq.sql 2018-02-18 06:31 1.4K
windowmaskerSdust.sql 2012-05-13 21:04 1.4K
extNcbiRefSeq.sql 2018-02-09 14:05 1.5K
multiz8way.sql 2012-05-13 20:58 1.5K
chainDanRer7Link.sql 2012-05-13 21:05 1.5K
chainGadMor1Link.sql 2012-05-13 20:52 1.5K
chainGasAcu1Link.sql 2012-05-13 20:53 1.5K
chainLatCha1Link.sql 2012-05-13 21:05 1.5K
chainOreNil1Link.sql 2012-05-13 21:01 1.5K
chainOryLat2Link.sql 2012-05-13 20:55 1.5K
chainTetNig2Link.sql 2012-05-13 20:57 1.5K
microsat.sql 2015-08-23 16:39 1.5K
phastConsElements8way.sql 2012-05-13 21:07 1.5K
history.sql 2012-05-13 20:51 1.5K
multiz8waySummary.sql 2012-05-13 21:07 1.5K
cytoBandIdeo.sql 2013-04-28 15:14 1.5K
gap.sql 2012-05-13 21:05 1.5K
chainMm10Link.sql 2013-08-04 13:03 1.5K
chainGalGal6Link.sql 2019-01-20 08:23 1.5K
chainXenTro9Link.sql 2017-12-14 10:20 1.5K
tableList.sql 2024-11-17 03:36 1.6K
seqNcbiRefSeq.sql 2018-02-09 14:05 1.6K
gold.sql 2012-05-13 20:47 1.6K
gbLoaded.sql 2020-08-19 09:27 1.6K
chainDanRer7.sql 2012-05-13 21:06 1.6K
chainGadMor1.sql 2012-05-13 20:47 1.6K
chainGasAcu1.sql 2012-05-13 21:06 1.6K
chainLatCha1.sql 2012-05-13 21:04 1.6K
chainOreNil1.sql 2012-05-13 20:47 1.6K
chainOryLat2.sql 2012-05-13 20:49 1.6K
chainTetNig2.sql 2012-05-13 21:04 1.6K
multiz8wayFrames.sql 2012-05-13 20:55 1.7K
genscan.sql 2013-12-09 23:13 1.7K
cpgIslandExt.sql 2019-04-14 03:21 1.7K
phyloP8way.sql 2012-05-13 20:47 1.7K
phastCons8way.sql 2012-05-13 20:49 1.7K
chainMm10.sql 2013-08-04 13:03 1.7K
chainGalGal6.sql 2019-01-20 08:23 1.7K
chainXenTro9.sql 2017-12-14 10:20 1.7K
cpgIslandExtUnmasked.sql 2019-04-14 03:21 1.7K
refFlat.sql 2020-08-19 09:22 1.7K
hgFindSpec.sql 2023-12-05 13:51 1.8K
estOrientInfo.sql 2019-03-17 09:27 1.8K
rmsk.sql 2012-05-13 21:07 1.8K
mrnaOrientInfo.sql 2020-08-19 09:22 1.8K
simpleRepeat.sql 2012-05-13 20:53 1.9K
nestedRepeats.sql 2012-05-13 20:51 1.9K
ensGene.sql 2019-02-10 03:41 1.9K
augustusGene.sql 2015-07-26 13:38 1.9K
refGene.sql 2020-08-19 09:22 1.9K
ncbiRefSeq.sql 2018-02-09 13:38 1.9K
ncbiRefSeqCurated.sql 2018-02-09 13:38 2.0K
ncbiRefSeqPredicted.sql 2018-02-09 13:38 2.0K
ncbiRefSeqLink.sql 2018-02-09 13:38 2.0K
netDanRer7.sql 2012-05-13 20:53 2.0K
netGadMor1.sql 2012-05-13 21:04 2.0K
netGasAcu1.sql 2012-05-13 20:53 2.0K
netLatCha1.sql 2012-05-13 20:49 2.0K
netOreNil1.sql 2012-05-13 21:01 2.0K
netOryLat2.sql 2012-05-13 21:05 2.0K
netTetNig2.sql 2012-05-13 20:50 2.0K
trackDb.sql 2023-12-05 13:51 2.1K
netMm10.sql 2013-08-04 13:04 2.1K
netGalGal6.sql 2019-01-20 08:23 2.1K
netXenTro9.sql 2017-12-14 10:21 2.1K
all_est.sql 2019-03-17 09:27 2.1K
intronEst.sql 2019-03-17 09:26 2.1K
all_mrna.sql 2020-05-06 13:45 2.1K
xenoMrna.sql 2020-08-19 09:10 2.1K
refSeqAli.sql 2020-08-19 09:23 2.1K
ncbiRefSeqPsl.sql 2018-02-09 13:38 2.1K
tableList.txt.gz 2024-11-17 03:36 4.7K
tableDescriptions.txt.gz 2024-11-16 02:03 7.6K
mrnaOrientInfo.txt.gz 2020-08-19 09:22 27K
cytoBandIdeo.txt.gz 2013-04-28 15:14 33K
chromInfo.txt.gz 2012-05-13 20:55 33K
gbLoaded.txt.gz 2020-08-19 09:27 41K
refFlat.txt.gz 2020-08-19 09:22 42K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:38 42K
trackDb.txt.gz 2023-12-05 13:51 43K
refGene.txt.gz 2020-08-19 09:22 47K
refSeqAli.txt.gz 2020-08-19 09:23 49K
ucscToINSDC.txt.gz 2019-02-10 03:41 50K
ucscToRefSeq.txt.gz 2018-02-18 06:31 52K
chromAlias.txt.gz 2019-02-10 03:41 66K
all_mrna.txt.gz 2020-05-06 13:45 75K
ensemblSource.txt.gz 2019-02-10 03:41 80K
microsat.txt.gz 2015-08-23 16:39 158K
ensemblToGeneName.txt.gz 2019-02-10 03:41 164K
ncbiRefSeqCds.txt.gz 2018-02-09 14:05 208K
gold.txt.gz 2012-05-13 20:47 268K
ensGtp.txt.gz 2019-02-10 03:41 295K
nestedRepeats.txt.gz 2012-05-13 20:51 298K
gap.txt.gz 2012-05-13 21:05 423K
seqNcbiRefSeq.txt.gz 2018-02-09 14:05 505K
cpgIslandExt.txt.gz 2019-04-14 03:21 726K
cpgIslandExtUnmasked.txt.gz 2019-04-14 03:21 1.0M
ncbiRefSeqLink.txt.gz 2018-02-09 13:38 1.0M
genscan.txt.gz 2013-12-09 23:13 1.3M
ensGene.txt.gz 2019-02-10 03:41 2.1M
multiz8waySummary.txt.gz 2012-05-13 21:07 2.3M
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:38 2.4M
augustusGene.txt.gz 2015-07-26 13:38 2.4M
ncbiRefSeq.txt.gz 2018-02-09 13:38 2.4M
ncbiRefSeqPsl.txt.gz 2018-02-09 13:38 2.9M
estOrientInfo.txt.gz 2019-03-17 09:27 3.1M
simpleRepeat.txt.gz 2012-05-13 20:53 3.4M
rmsk.txt.gz 2012-05-13 21:07 4.7M
chainMm10.txt.gz 2013-08-04 13:03 4.7M
netMm10.txt.gz 2013-08-04 13:04 4.8M
netXenTro9.txt.gz 2017-12-14 10:21 4.9M
netGalGal6.txt.gz 2019-01-20 08:23 5.0M
chainGalGal6.txt.gz 2019-01-20 08:23 5.2M
netLatCha1.txt.gz 2012-05-13 20:49 5.8M
ensPep.txt.gz 2019-02-10 03:41 7.3M
intronEst.txt.gz 2019-03-17 09:26 7.8M
ncbiRefSeqPepTable.txt.gz 2018-02-09 14:05 7.9M
netDanRer7.txt.gz 2012-05-13 20:53 8.3M
phastCons8way.txt.gz 2012-05-13 20:49 9.6M
netGadMor1.txt.gz 2012-05-13 21:04 9.8M
chainLatCha1.txt.gz 2012-05-13 21:04 10M
phastConsElements8way.txt.gz 2012-05-13 21:07 11M
phyloP8way.txt.gz 2012-05-13 20:47 11M
netOreNil1.txt.gz 2012-05-13 21:01 11M
chainTetNig2.txt.gz 2012-05-13 21:04 12M
chainXenTro9.txt.gz 2017-12-14 10:20 12M
netOryLat2.txt.gz 2012-05-13 21:05 12M
netGasAcu1.txt.gz 2012-05-13 20:53 13M
all_est.txt.gz 2019-03-17 09:27 13M
multiz8wayFrames.txt.gz 2012-05-13 20:55 14M
windowmaskerSdust.txt.gz 2012-05-13 21:04 15M
netTetNig2.txt.gz 2012-05-13 20:51 17M
chainGadMor1.txt.gz 2012-05-13 20:47 21M
chainDanRer7.txt.gz 2012-05-13 21:06 28M
chainGasAcu1.txt.gz 2012-05-13 21:06 29M
chainGalGal6Link.txt.gz 2019-01-20 08:23 30M
chainMm10Link.txt.gz 2013-08-04 13:03 31M
chainOreNil1.txt.gz 2012-05-13 20:47 31M
chainOryLat2.txt.gz 2012-05-13 20:49 32M
multiz8way.txt.gz 2012-05-13 20:58 37M
chainLatCha1Link.txt.gz 2012-05-13 21:05 41M
chainXenTro9Link.txt.gz 2017-12-14 10:20 47M
chainGadMor1Link.txt.gz 2012-05-13 20:52 92M
chainTetNig2Link.txt.gz 2012-05-13 20:58 106M
chainDanRer7Link.txt.gz 2012-05-13 21:05 109M
chainGasAcu1Link.txt.gz 2012-05-13 20:53 182M
chainOryLat2Link.txt.gz 2012-05-13 20:56 185M
chainOreNil1Link.txt.gz 2012-05-13 21:02 189M
xenoMrna.txt.gz 2020-08-19 09:10 192M