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 - all_est.sql 2019-03-17 09:27 2.1K all_est.txt.gz 2019-03-17 09:27 13M all_mrna.sql 2020-05-06 13:45 2.1K all_mrna.txt.gz 2020-05-06 13:45 75K augustusGene.sql 2015-07-26 13:38 1.9K augustusGene.txt.gz 2015-07-26 13:38 2.4M bigFiles.sql 2021-05-02 03:11 1.4K bigFiles.txt.gz 2021-05-02 03:11 64 chainDanRer7.sql 2012-05-13 21:06 1.6K chainDanRer7.txt.gz 2012-05-13 21:06 28M chainDanRer7Link.sql 2012-05-13 21:05 1.5K chainDanRer7Link.txt.gz 2012-05-13 21:05 109M chainGadMor1.sql 2012-05-13 20:47 1.6K chainGadMor1.txt.gz 2012-05-13 20:47 21M chainGadMor1Link.sql 2012-05-13 20:52 1.5K chainGadMor1Link.txt.gz 2012-05-13 20:52 92M 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 chainGasAcu1.sql 2012-05-13 21:06 1.6K chainGasAcu1.txt.gz 2012-05-13 21:06 29M chainGasAcu1Link.sql 2012-05-13 20:53 1.5K chainGasAcu1Link.txt.gz 2012-05-13 20:53 182M 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 chainLatCha1Link.txt.gz 2012-05-13 21:05 41M 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 chainOreNil1.sql 2012-05-13 20:47 1.6K chainOreNil1.txt.gz 2012-05-13 20:47 31M chainOreNil1Link.sql 2012-05-13 21:01 1.5K chainOreNil1Link.txt.gz 2012-05-13 21:02 189M chainOryLat2.sql 2012-05-13 20:49 1.6K chainOryLat2.txt.gz 2012-05-13 20:49 32M chainOryLat2Link.sql 2012-05-13 20:55 1.5K chainOryLat2Link.txt.gz 2012-05-13 20:56 185M chainTetNig2.sql 2012-05-13 21:04 1.6K chainTetNig2.txt.gz 2012-05-13 21:04 12M chainTetNig2Link.sql 2012-05-13 20:57 1.5K chainTetNig2Link.txt.gz 2012-05-13 20:58 106M 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 chromAlias.sql 2019-02-10 03:41 1.4K chromAlias.txt.gz 2019-02-10 03:41 66K chromInfo.sql 2012-05-13 20:55 1.3K chromInfo.txt.gz 2012-05-13 20:55 33K 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 cytoBandIdeo.sql 2013-04-28 15:14 1.5K cytoBandIdeo.txt.gz 2013-04-28 15:14 33K ensGene.sql 2019-02-10 03:41 1.9K ensGene.txt.gz 2019-02-10 03:41 2.1M ensGtp.sql 2019-02-10 03:41 1.4K ensGtp.txt.gz 2019-02-10 03:41 295K ensPep.sql 2019-02-10 03:41 1.3K ensPep.txt.gz 2019-02-10 03:41 7.3M ensemblSource.sql 2019-02-10 03:41 1.3K ensemblSource.txt.gz 2019-02-10 03:41 80K ensemblToGeneName.sql 2019-02-10 03:41 1.4K ensemblToGeneName.txt.gz 2019-02-10 03:41 164K estOrientInfo.sql 2019-03-17 09:27 1.8K estOrientInfo.txt.gz 2019-03-17 09:27 3.1M 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 gbLoaded.sql 2020-08-19 09:27 1.6K gbLoaded.txt.gz 2020-08-19 09:27 41K gc5BaseBw.sql 2012-05-13 20:59 1.2K gc5BaseBw.txt.gz 2012-05-13 20:59 59 genscan.sql 2013-12-09 23:13 1.7K genscan.txt.gz 2013-12-09 23:13 1.3M gold.sql 2012-05-13 20:47 1.6K gold.txt.gz 2012-05-13 20:47 268K grp.sql 2014-03-02 03:40 1.3K grp.txt.gz 2014-03-02 03:40 208 hgFindSpec.sql 2021-01-21 09:35 1.8K hgFindSpec.txt.gz 2021-01-21 09:35 773 history.sql 2012-05-13 20:51 1.5K history.txt.gz 2012-05-13 20:51 1.0K intronEst.sql 2019-03-17 09:26 2.1K intronEst.txt.gz 2019-03-17 09:26 7.8M microsat.sql 2015-08-23 16:39 1.5K microsat.txt.gz 2015-08-23 16:39 158K mrnaOrientInfo.sql 2020-08-19 09:22 1.8K mrnaOrientInfo.txt.gz 2020-08-19 09:22 27K multiz8way.sql 2012-05-13 20:58 1.5K multiz8way.txt.gz 2012-05-13 20:58 37M multiz8wayFrames.sql 2012-05-13 20:55 1.7K multiz8wayFrames.txt.gz 2012-05-13 20:55 14M multiz8waySummary.sql 2012-05-13 21:07 1.5K multiz8waySummary.txt.gz 2012-05-13 21:07 2.3M nestedRepeats.sql 2012-05-13 20:51 1.9K nestedRepeats.txt.gz 2012-05-13 20:51 298K netDanRer7.sql 2012-05-13 20:53 2.0K netDanRer7.txt.gz 2012-05-13 20:53 8.3M netGadMor1.sql 2012-05-13 21:04 2.0K netGadMor1.txt.gz 2012-05-13 21:04 9.8M netGalGal6.sql 2019-01-20 08:23 2.1K netGalGal6.txt.gz 2019-01-20 08:23 5.0M netGasAcu1.sql 2012-05-13 20:53 2.0K netGasAcu1.txt.gz 2012-05-13 20:53 13M netLatCha1.sql 2012-05-13 20:49 2.0K netLatCha1.txt.gz 2012-05-13 20:49 5.8M netMm10.sql 2013-08-04 13:04 2.1K netMm10.txt.gz 2013-08-04 13:04 4.8M netOreNil1.sql 2012-05-13 21:01 2.0K netOreNil1.txt.gz 2012-05-13 21:01 11M netOryLat2.sql 2012-05-13 21:05 2.0K netOryLat2.txt.gz 2012-05-13 21:05 12M netTetNig2.sql 2012-05-13 20:50 2.0K netTetNig2.txt.gz 2012-05-13 20:51 17M netXenTro9.sql 2017-12-14 10:21 2.1K netXenTro9.txt.gz 2017-12-14 10:21 4.9M phastCons8way.sql 2012-05-13 20:49 1.7K phastCons8way.txt.gz 2012-05-13 20:49 9.6M phastConsElements8way.sql 2012-05-13 21:07 1.5K phastConsElements8way.txt.gz 2012-05-13 21:07 11M phyloP8way.sql 2012-05-13 20:47 1.7K phyloP8way.txt.gz 2012-05-13 20:47 11M refFlat.sql 2020-08-19 09:22 1.7K refFlat.txt.gz 2020-08-19 09:22 42K refGene.sql 2020-08-19 09:22 1.9K refGene.txt.gz 2020-08-19 09:22 47K refSeqAli.sql 2020-08-19 09:23 2.1K refSeqAli.txt.gz 2020-08-19 09:23 49K rmsk.sql 2012-05-13 21:07 1.8K rmsk.txt.gz 2012-05-13 21:07 4.7M simpleRepeat.sql 2012-05-13 20:53 1.9K simpleRepeat.txt.gz 2012-05-13 20:53 3.4M tableDescriptions.sql 2019-07-21 03:41 1.4K tableDescriptions.txt.gz 2019-07-21 03:41 6.6K tableList.sql 2021-05-02 03:11 1.6K tableList.txt.gz 2021-05-02 03:11 4.2K trackDb.sql 2021-01-21 09:35 2.1K trackDb.txt.gz 2021-01-21 09:35 54K ucscToINSDC.sql 2019-02-10 03:41 1.4K ucscToINSDC.txt.gz 2019-02-10 03:41 50K ucscToRefSeq.sql 2018-02-18 06:31 1.4K ucscToRefSeq.txt.gz 2018-02-18 06:31 52K windowmaskerSdust.sql 2012-05-13 21:04 1.4K windowmaskerSdust.txt.gz 2012-05-13 21:04 15M xenoMrna.sql 2020-08-19 09:10 2.1K xenoMrna.txt.gz 2020-08-19 09:10 192M