This directory contains a dump of the UCSC genome annotation database for
the Jul. 2007 Zv7 assembly of the zebrafish genome (danRer5) obtained from 
the Wellcome Trust Sanger Institute. The annotations were generated by UCSC 
and collaborators worldwide.

This assembly was produced by a collaboration between the
Wellcome Trust Sanger Institute in Cambridge, UK, the Max Planck Institute
for Developmental Biology in Tuebingen, Germany, the Netherlands Institute
for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands
and Yi Zhou and Leonard Zon from the Children's Hospital in Boston,
Massachusetts.

For more information on the zebrafish genome, see the project website:
http://www.sanger.ac.uk/Projects/D_rerio/

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=danRer5
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/danRer5/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/danRer5/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer5/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer5/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer5/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 danRer5 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql danRer5 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

The Zv7 zebrafish sequence data were produced by the Zebrafish Sequencing
Group at the Sanger Institute and can be obtained directly from
ftp://ftp.ensembl.org/pub/assembly/zebrafish/Zv7release/. All sequence
data are made available before scientific publication with the understanding
that the groups involved in generating the data intend to publish the
initial large-scale analyses of the dataset. This will include a summary
detailing the data that have beeen generated and key features of the
genome identified from genomic assembly and clone mapping/sequencing. Any
redistribution of the data should carry this notice.

All the files and tables in this directory are freely usable for any purpose.
      Name                          Last modified      Size  Description
Parent Directory - bigFiles.txt.gz 2024-07-14 03:20 33 extFile.txt.gz 2007-10-15 10:28 129 grp.txt.gz 2014-03-02 03:40 208 history.txt.gz 2007-10-15 10:34 907 vegaPep.sql 2007-10-15 10:47 1.1K chromInfo.sql 2007-10-15 10:27 1.2K vegaToCloneId.sql 2007-10-15 10:47 1.2K ensPep.sql 2009-09-27 08:01 1.3K extFile.sql 2007-10-15 10:28 1.3K hgFindSpec.txt.gz 2023-03-28 13:48 1.4K grp.sql 2014-03-02 03:40 1.4K ensGtp.sql 2009-09-27 08:00 1.4K bigFiles.sql 2024-07-14 03:20 1.4K history.sql 2007-10-15 10:34 1.4K chainFr2Link.sql 2007-10-15 10:01 1.4K chainMm9Link.sql 2007-10-15 10:05 1.4K ctgPos2.sql 2007-10-15 10:27 1.4K seq.sql 2007-10-15 10:45 1.4K chainOryLat2Link.sql 2008-11-16 07:52 1.4K chainTetNig1Link.sql 2007-10-15 10:25 1.4K tableDescriptions.sql 2024-07-13 02:03 1.5K UMassME1Hotspot.sql 2011-11-06 09:43 1.5K UMassME3Hotspot.sql 2011-11-06 09:43 1.5K vegaInfoZfish.sql 2007-10-15 10:47 1.5K microsat.sql 2015-08-23 13:18 1.5K gap.sql 2007-10-15 10:28 1.5K chainHg19Link.sql 2009-10-04 07:34 1.5K chainMonDom5Link.sql 2009-09-27 08:01 1.5K tableList.sql 2024-07-14 03:20 1.6K gold.sql 2007-10-15 10:34 1.6K gbLoaded.sql 2020-08-21 09:14 1.6K chainFr2.sql 2007-10-15 10:00 1.6K chainMm9.sql 2007-10-15 10:05 1.6K chainOryLat2.sql 2008-11-16 07:51 1.7K chainTetNig1.sql 2007-10-15 10:25 1.7K tRNAs.sql 2012-04-22 21:08 1.7K UMassME1.sql 2011-11-06 09:43 1.7K UMassME3.sql 2011-11-06 09:43 1.7K UMassInput.sql 2011-11-06 09:43 1.7K UMassME1Peak.sql 2011-11-06 09:43 1.7K UMassME3Peak.sql 2011-11-06 09:43 1.7K gc5Base.sql 2007-10-15 10:34 1.7K refFlat.sql 2020-08-21 08:59 1.7K xenoRefFlat.sql 2020-08-21 08:59 1.7K hgFindSpec.sql 2023-03-28 13:48 1.8K estOrientInfo.sql 2017-11-26 06:44 1.8K chainHg19.sql 2009-10-04 07:34 1.8K chainMonDom5.sql 2009-09-27 08:01 1.8K mrnaOrientInfo.sql 2020-08-21 09:12 1.8K affyZonWildType.sql 2007-10-15 09:57 1.8K rmsk.sql 2007-10-15 10:41 1.9K affyTargetZonWildType.sql 2007-10-15 09:56 1.9K nestedRepeats.sql 2007-10-15 10:37 1.9K vegaGene.sql 2007-10-15 10:46 1.9K simpleRepeat.sql 2007-10-15 10:45 1.9K mgcGenes.sql 2020-03-01 05:36 1.9K vegaPseudoGene.sql 2007-10-15 10:47 1.9K augustusGene.sql 2015-07-26 11:52 1.9K refGene.sql 2020-08-21 08:56 1.9K xenoRefGene.sql 2020-08-21 08:59 2.0K ensGene.sql 2009-09-27 08:00 2.0K trackDb.sql 2023-03-28 13:48 2.1K all_est.sql 2017-11-26 06:44 2.1K xenoMrna.sql 2016-02-21 12:56 2.1K intronEst.sql 2017-11-26 06:44 2.1K mgcFullMrna.sql 2020-03-01 05:36 2.1K all_mrna.sql 2020-08-21 08:49 2.1K refSeqAli.sql 2020-08-21 09:12 2.1K xenoRefSeqAli.sql 2020-08-21 09:14 2.1K affyZebrafishTarget.sql 2007-10-15 09:56 2.2K affyZebrafishConsensus.sql 2007-10-15 09:56 2.2K netFr2.sql 2007-10-15 10:38 2.2K netMm9.sql 2007-10-15 10:39 2.2K netOryLat2.sql 2008-11-16 07:56 2.2K netTetNig1.sql 2007-10-15 10:40 2.2K blastHg18KG.sql 2009-12-20 10:59 2.3K netHg19.sql 2009-10-04 07:34 2.3K netMonDom5.sql 2009-09-27 08:01 2.3K vegaPseudoGene.txt.gz 2007-10-15 10:47 3.5K tableList.txt.gz 2024-07-14 03:20 4.6K tableDescriptions.txt.gz 2024-07-13 02:03 6.6K chromInfo.txt.gz 2007-10-15 10:27 28K trackDb.txt.gz 2023-03-28 13:48 36K gbLoaded.txt.gz 2020-08-21 09:14 43K vegaToCloneId.txt.gz 2007-10-15 10:47 56K gold.txt.gz 2007-10-15 10:34 86K tRNAs.txt.gz 2012-04-22 21:08 268K vegaInfoZfish.txt.gz 2007-10-15 10:47 339K ensGtp.txt.gz 2009-09-27 08:00 364K seq.txt.gz 2007-10-15 10:45 365K UMassME3Hotspot.txt.gz 2011-11-06 09:43 408K gap.txt.gz 2007-10-15 10:28 538K UMassME1Hotspot.txt.gz 2011-11-06 09:43 560K UMassME3Peak.txt.gz 2011-11-06 09:43 565K affyZebrafishTarget.txt.gz 2007-10-15 09:57 717K UMassME1Peak.txt.gz 2011-11-06 09:43 750K mrnaOrientInfo.txt.gz 2020-08-21 09:12 827K ctgPos2.txt.gz 2007-10-15 10:27 835K vegaGene.txt.gz 2007-10-15 10:46 1.0M affyZebrafishConsensus.txt.gz 2007-10-15 09:56 1.1M microsat.txt.gz 2015-08-23 13:18 1.1M mgcGenes.txt.gz 2020-03-01 05:36 1.2M UMassME3.txt.gz 2011-11-06 09:43 1.5M refFlat.txt.gz 2020-08-21 08:59 1.5M mgcFullMrna.txt.gz 2020-03-01 05:36 1.5M affyTargetZonWildType.txt.gz 2007-10-15 09:56 1.7M refSeqAli.txt.gz 2020-08-21 09:12 1.7M refGene.txt.gz 2020-08-21 08:56 1.7M affyZonWildType.txt.gz 2007-10-15 09:57 1.9M vegaPep.txt.gz 2007-10-15 10:47 2.1M UMassInput.txt.gz 2011-11-06 09:43 2.4M ensGene.txt.gz 2009-09-27 08:00 2.5M all_mrna.txt.gz 2020-08-21 08:49 2.6M UMassME1.txt.gz 2011-11-06 09:43 2.6M augustusGene.txt.gz 2015-07-26 11:52 2.8M blastHg18KG.txt.gz 2009-12-20 11:00 3.0M gc5Base.txt.gz 2007-10-15 10:34 5.6M ensPep.txt.gz 2009-09-27 08:01 7.4M netMm9.txt.gz 2007-10-15 10:39 7.5M netHg19.txt.gz 2009-10-04 07:34 8.2M netMonDom5.txt.gz 2009-09-27 08:01 8.3M chainMm9.txt.gz 2007-10-15 10:05 9.1M netTetNig1.txt.gz 2007-10-15 10:40 10M chainHg19.txt.gz 2009-10-04 07:34 10M chainTetNig1.txt.gz 2007-10-15 10:25 11M netFr2.txt.gz 2007-10-15 10:38 11M nestedRepeats.txt.gz 2007-10-15 10:38 11M chainFr2.txt.gz 2007-10-15 10:00 15M netOryLat2.txt.gz 2008-11-16 07:56 16M xenoRefSeqAli.txt.gz 2020-08-21 09:14 19M chainMonDom5.txt.gz 2009-09-27 08:01 19M xenoRefFlat.txt.gz 2020-08-21 08:59 20M estOrientInfo.txt.gz 2017-11-26 06:44 20M xenoRefGene.txt.gz 2020-08-21 08:59 22M simpleRepeat.txt.gz 2007-10-15 10:46 25M intronEst.txt.gz 2017-11-26 06:44 54M chainOryLat2.txt.gz 2008-11-16 07:52 62M chainTetNig1Link.txt.gz 2007-10-15 10:26 63M chainHg19Link.txt.gz 2009-10-04 07:34 65M chainMm9Link.txt.gz 2007-10-15 10:07 67M all_est.txt.gz 2017-11-26 06:44 85M rmsk.txt.gz 2007-10-15 10:43 87M chainFr2Link.txt.gz 2007-10-15 10:03 93M chainMonDom5Link.txt.gz 2009-09-27 08:01 95M xenoMrna.txt.gz 2016-02-21 12:56 213M chainOryLat2Link.txt.gz 2008-11-16 07:54 317M