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 2024-06-22 02:03 1.5K tableDescriptions.txt.gz 2024-06-22 02:03 7.6K tableList.sql 2024-06-23 03:29 1.6K tableList.txt.gz 2024-06-23 03:29 4.7K bigFiles.sql 2024-06-23 03:29 1.4K bigFiles.txt.gz 2024-06-23 03:29 90