This directory contains a dump of the UCSC genome annotation database for the
    Sep. 2014 (GRCz10/danRer10) assembly of the zebrafish genome
    (danRer10, Genome Reference Consortium Zebrafish Build 10) .

The annotations were generated by UCSC and collaborators worldwide.

For more information about this assembly, please note the NCBI resources:
    http://www.ncbi.nlm.nih.gov/genome/50
    http://www.ncbi.nlm.nih.gov/genome/assembly/210611
    http://www.ncbi.nlm.nih.gov/bioproject/13922

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=danRer10
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/danRer10/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/danRer10/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer10/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer10/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer10/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 danRer10 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql danRer10 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

-----------------------------------------------------------------------------
GenBank Data Usage

The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.

      Name                        Last modified      Size  Description
Parent Directory - chainHg38.sql 2015-04-01 15:00 1.7K chainHg38.txt.gz 2015-04-01 15:00 200M chainHg38Link.sql 2015-04-01 15:02 1.5K chainHg38Link.txt.gz 2015-04-01 15:03 734M chromInfo.sql 2015-04-01 15:06 1.4K chromInfo.txt.gz 2015-04-01 15:06 6.8K cpgIslandExt.sql 2015-04-01 15:06 1.7K cpgIslandExt.txt.gz 2015-04-01 15:06 250K cpgIslandExtUnmasked.sql 2015-04-01 15:06 1.7K cpgIslandExtUnmasked.txt.gz 2015-04-01 15:06 957K genscan.sql 2015-04-01 15:06 1.7K genscan.txt.gz 2015-04-01 15:06 2.4M cytoBandIdeo.sql 2015-04-01 15:06 1.5K cytoBandIdeo.txt.gz 2015-04-01 15:06 6.3K gold.sql 2015-04-01 15:06 1.7K gold.txt.gz 2015-04-01 15:06 641K grp.sql 2015-04-01 15:06 1.3K grp.txt.gz 2015-04-01 15:06 213 gap.sql 2015-04-01 15:06 1.6K gap.txt.gz 2015-04-01 15:06 244K nestedRepeats.sql 2015-04-01 15:06 1.9K nestedRepeats.txt.gz 2015-04-01 15:06 8.1M history.sql 2015-04-01 15:06 1.6K history.txt.gz 2015-04-01 15:06 441 netHg38.sql 2015-04-01 15:07 2.1K netHg38.txt.gz 2015-04-01 15:07 10M gc5BaseBw.sql 2015-04-01 15:08 1.3K gc5BaseBw.txt.gz 2015-04-01 15:08 67 rmsk.sql 2015-04-01 15:09 1.9K rmsk.txt.gz 2015-04-01 15:09 93M simpleRepeat.sql 2015-04-01 15:09 1.9K simpleRepeat.txt.gz 2015-04-01 15:09 25M ucscToINSDC.sql 2015-04-01 15:09 1.4K ucscToINSDC.txt.gz 2015-04-01 15:09 8.6K windowmaskerSdust.sql 2015-04-01 15:09 1.5K windowmaskerSdust.txt.gz 2015-04-01 15:09 80M augustusGene.sql 2015-07-26 11:52 1.9K augustusGene.txt.gz 2015-07-26 11:52 2.7M microsat.sql 2015-08-23 12:56 1.5K microsat.txt.gz 2015-08-23 12:56 1.0M chainGalGal5Link.sql 2016-09-18 07:35 1.6K chainGalGal5Link.txt.gz 2016-09-18 07:35 55M chainGalGal5.sql 2016-09-18 07:35 1.7K chainGalGal5.txt.gz 2016-09-18 07:35 12M netGalGal5.sql 2016-09-18 07:35 2.1K netGalGal5.txt.gz 2016-09-18 07:35 6.3M chainMelGal5.sql 2017-03-19 16:57 1.7K chainMelGal5.txt.gz 2017-03-19 16:57 5.9M netMelGal5.sql 2017-03-19 16:57 2.1K netMelGal5.txt.gz 2017-03-19 16:57 4.8M chainMelGal5Link.sql 2017-03-19 16:58 1.6K chainMelGal5Link.txt.gz 2017-03-19 16:58 20M chainRn6.sql 2017-03-26 19:02 1.7K chainRn6.txt.gz 2017-03-26 19:02 60M chainRn6Link.sql 2017-03-26 19:04 1.5K chainRn6Link.txt.gz 2017-03-26 19:07 291M netRn6.sql 2017-03-26 19:16 2.1K netRn6.txt.gz 2017-03-26 19:16 9.4M chromAlias.sql 2017-09-03 05:24 1.4K chromAlias.txt.gz 2017-09-03 05:24 12K intronEst.sql 2017-11-26 06:39 2.1K intronEst.txt.gz 2017-11-26 06:39 51M estOrientInfo.sql 2017-11-26 06:39 1.8K estOrientInfo.txt.gz 2017-11-26 06:40 17M all_est.sql 2017-11-26 06:40 2.1K all_est.txt.gz 2017-11-26 06:40 73M ensGtp.sql 2018-02-04 06:19 1.4K ensGtp.txt.gz 2018-02-04 06:19 706K ensGene.sql 2018-02-04 06:19 1.9K ensGene.txt.gz 2018-02-04 06:19 4.0M ensPep.sql 2018-02-04 06:19 1.3K ensPep.txt.gz 2018-02-04 06:19 13M ensemblSource.sql 2018-02-04 06:19 1.4K ensemblSource.txt.gz 2018-02-04 06:19 207K ensemblToGeneName.sql 2018-02-04 06:19 1.4K ensemblToGeneName.txt.gz 2018-02-04 06:19 458K ucscToRefSeq.sql 2018-02-18 06:01 1.4K ucscToRefSeq.txt.gz 2018-02-18 06:01 9.7K extNcbiRefSeq.sql 2018-04-08 05:49 1.4K extNcbiRefSeq.txt.gz 2018-04-08 05:49 92 ncbiRefSeq.sql 2018-04-08 05:49 1.9K ncbiRefSeq.txt.gz 2018-04-08 05:49 3.7M ncbiRefSeqCds.sql 2018-04-08 05:49 1.3K ncbiRefSeqCds.txt.gz 2018-04-08 05:49 324K ncbiRefSeqCurated.sql 2018-04-08 05:49 2.0K ncbiRefSeqCurated.txt.gz 2018-04-08 05:49 1.5M ncbiRefSeqLink.sql 2018-04-08 05:49 2.0K ncbiRefSeqLink.txt.gz 2018-04-08 05:49 1.9M ncbiRefSeqOther.sql 2018-04-08 05:49 1.3K ncbiRefSeqOther.txt.gz 2018-04-08 05:49 76 ncbiRefSeqPepTable.sql 2018-04-08 05:49 1.4K ncbiRefSeqPepTable.txt.gz 2018-04-08 05:49 13M ncbiRefSeqPredicted.sql 2018-04-08 05:49 2.0K ncbiRefSeqPredicted.txt.gz 2018-04-08 05:49 2.6M ncbiRefSeqPsl.sql 2018-04-08 05:49 2.1K ncbiRefSeqPsl.txt.gz 2018-04-08 05:49 4.5M seqNcbiRefSeq.sql 2018-04-08 05:49 1.5K seqNcbiRefSeq.txt.gz 2018-04-08 05:49 844K grcIncidentDb.sql 2018-05-13 04:55 1.3K grcIncidentDb.txt.gz 2018-05-13 04:55 78 mmBlastTab.sql 2018-05-21 16:02 1.7K mmBlastTab.txt.gz 2018-05-21 16:02 339K mgcGenes.sql 2020-03-01 05:32 1.9K mgcGenes.txt.gz 2020-03-01 05:32 1.2M mgcFullMrna.sql 2020-03-01 05:32 2.1K mgcFullMrna.txt.gz 2020-03-01 05:32 1.5M all_mrna.sql 2020-08-18 21:22 2.1K all_mrna.txt.gz 2020-08-18 21:22 2.4M xenoMrna.sql 2020-08-18 21:22 2.1K xenoMrna.txt.gz 2020-08-18 21:22 131M refGene.sql 2020-08-18 21:59 1.9K refGene.txt.gz 2020-08-18 21:59 1.7M refFlat.sql 2020-08-18 21:59 1.7K refFlat.txt.gz 2020-08-18 21:59 1.5M xenoRefGene.sql 2020-08-18 21:59 2.0K xenoRefGene.txt.gz 2020-08-18 21:59 13M xenoRefFlat.sql 2020-08-18 21:59 1.7K xenoRefFlat.txt.gz 2020-08-18 21:59 12M mrnaOrientInfo.sql 2020-08-18 21:59 1.8K mrnaOrientInfo.txt.gz 2020-08-18 21:59 764K refSeqAli.sql 2020-08-18 21:59 2.1K refSeqAli.txt.gz 2020-08-18 21:59 1.6M xenoRefSeqAli.sql 2020-08-18 21:59 2.2K xenoRefSeqAli.txt.gz 2020-08-18 21:59 11M gbLoaded.sql 2020-08-18 21:59 1.6K gbLoaded.txt.gz 2020-08-18 21:59 42K crisprAllTargets.sql 2023-11-06 10:50 1.3K crisprAllTargets.txt.gz 2023-11-06 10:50 70 trackDb.sql 2023-12-05 13:51 2.1K trackDb.txt.gz 2023-12-05 13:51 35K trackDb_pushedout.sql 2023-12-05 13:51 2.1K trackDb_pushedout.txt.gz 2023-12-05 13:51 35K hgFindSpec.sql 2023-12-05 13:51 1.8K hgFindSpec.txt.gz 2023-12-05 13:51 1.3K hgFindSpec_pushedout.sql 2023-12-05 13:51 1.8K hgFindSpec_pushedout.txt.gz 2023-12-05 13:51 1.3K tableDescriptions.sql 2024-03-23 02:03 1.4K tableDescriptions.txt.gz 2024-03-23 02:03 6.9K tableList.sql 2024-03-24 03:08 1.6K tableList.txt.gz 2024-03-24 03:08 4.1K bigFiles.sql 2024-03-24 03:08 1.4K bigFiles.txt.gz 2024-03-24 03:08 145