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