This directory contains a dump of the UCSC genome annotation database for
the May. 2010 (Genofisk GadMor_May2010/gadMor1) assembly of the atlantic cod genome
(gadMor1, Genofisk GadMor_May2010 (GCA_000231765.1)).
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/2661
    http://www.ncbi.nlm.nih.gov/genome/assembly/311358
    http://www.ncbi.nlm.nih.gov/bioproject/41391

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=gadMor1
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/gadMor1/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/gadMor1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/gadMor1/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/gadMor1/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/gadMor1/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 gadMor1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql gadMor1 --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 - xenoRefSeqAli.txt.gz 2020-08-19 10:11 29M xenoRefSeqAli.sql 2020-08-19 10:11 2.1K xenoRefGene.txt.gz 2020-08-19 10:11 31M xenoRefGene.sql 2020-08-19 10:11 2.0K xenoRefFlat.txt.gz 2020-08-19 10:11 27M xenoRefFlat.sql 2020-08-19 10:11 1.7K windowmaskerSdust.txt.gz 2012-11-06 14:10 30M windowmaskerSdust.sql 2012-11-06 14:10 1.5K ucscToINSDC.txt.gz 2013-09-15 13:09 3.0M ucscToINSDC.sql 2013-09-15 13:09 1.4K ucscToEnsembl.txt.gz 2013-08-11 03:46 2.0M ucscToEnsembl.sql 2013-08-11 03:46 1.4K trackDb_pushedout.txt.gz 2021-12-27 12:20 36K trackDb_pushedout.sql 2021-12-27 12:20 2.1K trackDb.txt.gz 2023-03-28 13:49 38K trackDb.sql 2023-03-28 13:49 2.1K tableList.txt.gz 2024-03-24 03:43 2.7K tableList.sql 2024-03-24 03:43 1.6K tableDescriptions.txt.gz 2024-03-23 02:03 5.5K tableDescriptions.sql 2024-03-23 02:03 1.4K simpleRepeat.txt.gz 2012-11-06 14:10 21M simpleRepeat.sql 2012-11-06 14:10 1.9K rmsk.txt.gz 2012-11-06 14:11 15M rmsk.sql 2012-11-06 14:11 1.9K netMm10.txt.gz 2012-11-06 14:10 5.5M netMm10.sql 2012-11-06 14:10 2.1K netFr3.txt.gz 2012-11-06 14:10 14M netFr3.sql 2012-11-06 14:10 2.1K nestedRepeats.txt.gz 2012-11-06 14:10 304K nestedRepeats.sql 2012-11-06 14:10 1.9K mrnaOrientInfo.txt.gz 2020-08-19 10:05 841K mrnaOrientInfo.sql 2020-08-19 10:05 1.8K microsat.txt.gz 2015-08-23 16:40 1.4M microsat.sql 2015-08-23 16:40 1.5K intronEst.txt.gz 2016-05-15 08:41 4.7M intronEst.sql 2016-05-15 08:41 2.1K history.txt.gz 2012-11-06 14:10 551 history.sql 2012-11-06 14:10 1.6K hgFindSpec_pushedout.txt.gz 2021-12-27 12:20 798 hgFindSpec_pushedout.sql 2021-12-27 12:20 1.8K hgFindSpec.txt.gz 2023-03-28 13:49 837 hgFindSpec.sql 2023-03-28 13:49 1.8K grp.txt.gz 2014-03-02 03:41 208 grp.sql 2014-03-02 03:41 1.3K gold.txt.gz 2012-11-06 14:10 6.1M gold.sql 2012-11-06 14:10 1.7K genscan.txt.gz 2012-11-06 14:10 1.9M genscan.sql 2012-11-06 14:10 1.7K gc5BaseBw.txt.gz 2012-11-06 14:11 63 gc5BaseBw.sql 2012-11-06 14:11 1.3K gbLoaded.txt.gz 2020-08-19 10:11 44K gbLoaded.sql 2020-08-19 10:11 1.6K gap.txt.gz 2012-11-06 14:11 1.7M gap.sql 2012-11-06 14:11 1.6K estOrientInfo.txt.gz 2016-05-15 08:41 3.7M estOrientInfo.sql 2016-05-15 08:41 1.8K ensemblToGeneName.txt.gz 2019-02-10 03:41 121K ensemblToGeneName.sql 2019-02-10 03:41 1.4K ensemblSource.txt.gz 2019-02-10 03:41 61K ensemblSource.sql 2019-02-10 03:41 1.4K ensemblGeneScaffold.txt.gz 2019-02-10 03:41 2.6M ensemblGeneScaffold.sql 2019-02-10 03:41 1.7K ensPep.txt.gz 2019-02-10 03:41 5.5M ensPep.sql 2019-02-10 03:41 1.3K ensGtp.txt.gz 2019-02-10 03:41 230K ensGtp.sql 2019-02-10 03:41 1.4K ensGene.txt.gz 2019-02-10 03:41 2.9M ensGene.sql 2019-02-10 03:41 1.9K cytoBandIdeo.txt.gz 2013-04-28 15:14 1.9M cytoBandIdeo.sql 2013-04-28 15:14 1.5K cpgIslandExtUnmasked.txt.gz 2014-06-01 13:15 1.8M cpgIslandExtUnmasked.sql 2014-06-01 13:15 1.7K cpgIslandExt.txt.gz 2012-11-06 14:10 1.0M cpgIslandExt.sql 2012-11-06 14:10 1.7K chromInfo.txt.gz 2012-11-06 14:10 1.8M chromInfo.sql 2012-11-06 14:10 1.4K chromAlias.txt.gz 2018-08-05 06:36 2.1M chromAlias.sql 2018-08-05 06:36 1.4K chainMm10Link.txt.gz 2012-11-06 14:11 35M chainMm10Link.sql 2012-11-06 14:11 1.5K chainMm10.txt.gz 2012-11-06 14:12 7.1M chainMm10.sql 2012-11-06 14:12 1.7K chainFr3Link.txt.gz 2012-11-06 14:10 93M chainFr3Link.sql 2012-11-06 14:10 1.5K chainFr3.txt.gz 2012-11-06 14:09 20M chainFr3.sql 2012-11-06 14:09 1.7K bigFiles.txt.gz 2024-03-24 03:43 68 bigFiles.sql 2024-03-24 03:43 1.4K augustusGene.txt.gz 2015-07-26 13:39 3.0M augustusGene.sql 2015-07-26 13:39 1.9K all_mrna.txt.gz 2020-08-19 10:05 3.1M all_mrna.sql 2020-08-19 10:05 2.1K all_est.txt.gz 2016-05-15 08:41 14M all_est.sql 2016-05-15 08:41 2.1K