This directory contains a dump of the UCSC genome annotation database for the
    May 2017 (GRCz11/danRer11) assembly of the zebrafish genome
    (danRer11, Genome Reference Consortium) .

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/1104621
    http://www.ncbi.nlm.nih.gov/bioproject/11776

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=danRer11
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.soe.ucsc.edu, then go to
the directory goldenPath/danRer11/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.soe.ucsc.edu/goldenPath/danRer11/database/ .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/danRer11/database/gc5Base.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/danRer11/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/danRer11/database/gc5Base.txt.gz' 
        -O gc5Base.txt.gz

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 danRer11 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql danRer11 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

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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 - gc5BaseBw.txt.gz 2017-11-01 13:04 67 ncbiRefSeqOther.txt.gz 2020-05-10 03:27 76 grcIncidentDb.txt.gz 2019-09-22 03:19 78 extNcbiRefSeq.txt.gz 2020-05-10 03:27 92 bigFiles.txt.gz 2022-08-14 03:04 121 grp.txt.gz 2017-11-01 13:04 213 history.txt.gz 2017-11-01 13:05 606 hgFindSpec.txt.gz 2022-05-06 12:33 1.2K hgFindSpec_pushedout.txt.gz 2022-04-26 10:29 1.2K gc5BaseBw.sql 2017-11-01 13:04 1.3K grcIncidentDb.sql 2019-09-22 03:19 1.3K ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K ensPep.sql 2019-02-10 03:41 1.3K ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K grp.sql 2017-11-01 13:04 1.3K ensemblLift.sql 2019-01-13 04:04 1.4K ensemblSource.sql 2019-02-10 03:41 1.4K ucscToEnsembl.sql 2019-01-13 04:04 1.4K ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K bigFiles.sql 2022-08-14 03:04 1.4K ensemblToGeneName.sql 2019-02-10 03:41 1.4K chromInfo.sql 2017-11-01 13:03 1.4K ensGtp.sql 2019-02-10 03:41 1.4K chromAlias.sql 2018-08-05 06:11 1.4K tableDescriptions.sql 2022-02-10 06:34 1.4K ucscToINSDC.sql 2017-11-01 13:03 1.4K ucscToRefSeq.sql 2017-11-01 13:03 1.4K extNcbiRefSeq.sql 2020-05-10 03:27 1.4K microsat.sql 2017-11-01 13:02 1.5K windowmaskerSdust.sql 2017-11-01 13:03 1.5K cytoBandIdeo.sql 2017-11-01 13:03 1.5K chainHg38Link.sql 2017-11-01 13:00 1.5K chainMm10Link.sql 2017-11-01 13:03 1.5K seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K chainGalGal6Link.sql 2019-01-20 08:06 1.6K chainMm39Link.sql 2020-11-25 02:49 1.6K tableList.sql 2022-08-14 03:04 1.6K genscanSubopt.sql 2017-11-01 13:04 1.6K history.sql 2017-11-01 13:05 1.6K gbLoaded.sql 2020-08-18 22:17 1.6K gap.sql 2017-11-01 13:03 1.6K gold.sql 2017-11-01 13:03 1.7K genscan.sql 2017-11-01 13:04 1.7K cpgIslandExt.sql 2017-11-01 13:03 1.7K hgBlastTab.sql 2022-07-12 17:02 1.7K mmBlastTab.sql 2022-07-12 17:09 1.7K chainHg38.sql 2017-11-01 12:59 1.7K chainMm10.sql 2017-11-01 13:02 1.7K refFlat.sql 2020-08-18 21:59 1.7K chainGalGal6.sql 2019-01-20 08:06 1.7K cpgIslandExtUnmasked.sql 2017-11-01 13:03 1.7K xenoRefFlat.sql 2020-08-18 21:59 1.7K chainMm39.sql 2020-11-25 02:48 1.7K hgFindSpec.sql 2022-05-06 12:33 1.8K estOrientInfo.sql 2017-11-26 06:41 1.8K mrnaOrientInfo.sql 2020-08-18 22:14 1.8K hgFindSpec_pushedout.sql 2022-04-26 10:29 1.8K rmsk.sql 2017-11-01 12:58 1.9K ensGene.sql 2019-02-10 03:41 1.9K refGene.sql 2020-08-18 21:59 1.9K simpleRepeat.sql 2017-11-01 12:59 1.9K ncbiRefSeq.sql 2020-05-10 03:27 1.9K nestedRepeats.sql 2017-11-01 13:03 1.9K xenoRefGene.sql 2020-08-18 21:59 1.9K augustusGene.sql 2017-11-01 12:58 1.9K ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K trackDb.sql 2022-05-06 12:33 2.1K trackDb_pushedout.sql 2022-04-26 10:29 2.1K netHg38.sql 2017-11-01 13:03 2.1K netMm10.sql 2017-11-01 13:03 2.1K netGalGal6.sql 2019-01-20 08:07 2.1K all_est.sql 2017-11-26 06:40 2.1K all_mrna.sql 2020-08-18 21:59 2.1K xenoMrna.sql 2020-08-18 21:59 2.1K intronEst.sql 2017-11-26 06:40 2.1K refSeqAli.sql 2020-08-18 22:14 2.1K netMm39.sql 2020-11-25 02:50 2.1K ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K xenoRefSeqAli.sql 2020-08-18 22:14 2.1K tableList.txt.gz 2022-08-14 03:04 4.1K ensemblLift.txt.gz 2019-01-13 04:04 6.8K tableDescriptions.txt.gz 2022-02-10 06:34 6.9K ucscToEnsembl.txt.gz 2019-01-13 04:04 9.7K cytoBandIdeo.txt.gz 2017-11-01 13:03 13K chromInfo.txt.gz 2017-11-01 13:03 14K ucscToINSDC.txt.gz 2017-11-01 13:03 17K ucscToRefSeq.txt.gz 2017-11-01 13:03 18K chromAlias.txt.gz 2018-08-05 06:11 20K gbLoaded.txt.gz 2020-08-18 22:17 28K trackDb.txt.gz 2022-05-06 12:33 52K trackDb_pushedout.txt.gz 2022-04-26 10:29 52K gap.txt.gz 2017-11-01 13:03 196K ensemblSource.txt.gz 2019-02-10 03:41 200K cpgIslandExt.txt.gz 2017-11-01 13:03 287K mmBlastTab.txt.gz 2022-07-12 17:09 348K hgBlastTab.txt.gz 2022-07-12 17:02 356K ncbiRefSeqCds.txt.gz 2020-05-10 03:27 370K ensemblToGeneName.txt.gz 2019-02-10 03:41 451K gold.txt.gz 2017-11-01 13:03 657K ensGtp.txt.gz 2019-02-10 03:41 687K mrnaOrientInfo.txt.gz 2020-08-18 22:14 869K seqNcbiRefSeq.txt.gz 2020-05-10 03:27 922K cpgIslandExtUnmasked.txt.gz 2017-11-01 13:03 1.1M microsat.txt.gz 2017-11-01 13:02 1.2M refFlat.txt.gz 2020-08-18 21:59 1.7M refSeqAli.txt.gz 2020-08-18 22:14 1.8M refGene.txt.gz 2020-08-18 21:59 1.9M ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 1.9M ncbiRefSeqLink.txt.gz 2020-05-10 03:27 2.4M genscan.txt.gz 2017-11-01 13:04 2.5M all_mrna.txt.gz 2020-08-18 21:59 2.8M ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 3.0M augustusGene.txt.gz 2017-11-01 12:58 3.3M ensGene.txt.gz 2019-02-10 03:41 3.8M genscanSubopt.txt.gz 2017-11-01 13:04 3.9M ncbiRefSeq.txt.gz 2020-05-10 03:27 4.4M ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 5.5M netMm10.txt.gz 2017-11-01 13:03 6.4M netHg38.txt.gz 2017-11-01 13:03 6.6M netMm39.txt.gz 2020-11-25 02:50 6.8M nestedRepeats.txt.gz 2017-11-01 13:03 9.8M chainMm39.txt.gz 2020-11-25 02:48 11M netGalGal6.txt.gz 2019-01-20 08:07 11M xenoRefSeqAli.txt.gz 2020-08-18 22:14 13M xenoRefFlat.txt.gz 2020-08-18 21:59 14M ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 14M ensPep.txt.gz 2019-02-10 03:41 15M xenoRefGene.txt.gz 2020-08-18 21:59 16M estOrientInfo.txt.gz 2017-11-26 06:41 20M chainGalGal6.txt.gz 2019-01-20 08:06 26M simpleRepeat.txt.gz 2017-11-01 12:59 29M chainMm10.txt.gz 2017-11-01 13:02 33M chainMm39Link.txt.gz 2020-11-25 02:49 41M intronEst.txt.gz 2017-11-26 06:40 59M chainMm10Link.txt.gz 2017-11-01 13:03 83M all_est.txt.gz 2017-11-26 06:40 84M chainGalGal6Link.txt.gz 2019-01-20 08:06 96M windowmaskerSdust.txt.gz 2017-11-01 13:03 99M rmsk.txt.gz 2017-11-01 12:58 113M xenoMrna.txt.gz 2020-08-18 21:59 153M chainHg38.txt.gz 2017-11-01 12:59 239M chainHg38Link.txt.gz 2017-11-01 13:01 554M