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.
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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;'
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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.
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All the files and tables in this directory are freely usable for any purpose.
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Name Last modified Size Description
Parent Directory -
chainFr3.sql 2012-11-06 14:09 1.7K
chainFr3.txt.gz 2012-11-06 14:09 20M
genscan.sql 2012-11-06 14:10 1.7K
genscan.txt.gz 2012-11-06 14:10 1.9M
history.sql 2012-11-06 14:10 1.6K
history.txt.gz 2012-11-06 14:10 551
windowmaskerSdust.sql 2012-11-06 14:10 1.5K
windowmaskerSdust.txt.gz 2012-11-06 14:10 30M
chainFr3Link.sql 2012-11-06 14:10 1.5K
chainFr3Link.txt.gz 2012-11-06 14:10 93M
netFr3.sql 2012-11-06 14:10 2.1K
netFr3.txt.gz 2012-11-06 14:10 14M
gold.sql 2012-11-06 14:10 1.7K
gold.txt.gz 2012-11-06 14:10 6.1M
chromInfo.sql 2012-11-06 14:10 1.4K
chromInfo.txt.gz 2012-11-06 14:10 1.8M
cpgIslandExt.sql 2012-11-06 14:10 1.7K
nestedRepeats.sql 2012-11-06 14:10 1.9K
nestedRepeats.txt.gz 2012-11-06 14:10 304K
cpgIslandExt.txt.gz 2012-11-06 14:10 1.0M
netMm10.sql 2012-11-06 14:10 2.1K
netMm10.txt.gz 2012-11-06 14:10 5.5M
simpleRepeat.sql 2012-11-06 14:10 1.9K
simpleRepeat.txt.gz 2012-11-06 14:10 21M
gc5BaseBw.sql 2012-11-06 14:11 1.3K
gc5BaseBw.txt.gz 2012-11-06 14:11 63
gap.sql 2012-11-06 14:11 1.6K
gap.txt.gz 2012-11-06 14:11 1.7M
rmsk.sql 2012-11-06 14:11 1.9K
rmsk.txt.gz 2012-11-06 14:11 15M
chainMm10Link.sql 2012-11-06 14:11 1.5K
chainMm10Link.txt.gz 2012-11-06 14:11 35M
chainMm10.sql 2012-11-06 14:12 1.7K
chainMm10.txt.gz 2012-11-06 14:12 7.1M
cytoBandIdeo.sql 2013-04-28 15:14 1.5K
cytoBandIdeo.txt.gz 2013-04-28 15:14 1.9M
ucscToEnsembl.sql 2013-08-11 03:46 1.4K
ucscToEnsembl.txt.gz 2013-08-11 03:46 2.0M
ucscToINSDC.sql 2013-09-15 13:09 1.4K
ucscToINSDC.txt.gz 2013-09-15 13:09 3.0M
grp.sql 2014-03-02 03:41 1.3K
grp.txt.gz 2014-03-02 03:41 208
cpgIslandExtUnmasked.sql 2014-06-01 13:15 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 13:15 1.8M
augustusGene.sql 2015-07-26 13:39 1.9K
augustusGene.txt.gz 2015-07-26 13:39 3.0M
microsat.sql 2015-08-23 16:40 1.5K
microsat.txt.gz 2015-08-23 16:40 1.4M
intronEst.sql 2016-05-15 08:41 2.1K
intronEst.txt.gz 2016-05-15 08:41 4.7M
all_est.sql 2016-05-15 08:41 2.1K
all_est.txt.gz 2016-05-15 08:41 14M
estOrientInfo.sql 2016-05-15 08:41 1.8K
estOrientInfo.txt.gz 2016-05-15 08:41 3.7M
chromAlias.sql 2018-08-05 06:36 1.4K
chromAlias.txt.gz 2018-08-05 06:36 2.1M
ensGene.sql 2019-02-10 03:41 1.9K
ensGene.txt.gz 2019-02-10 03:41 2.9M
ensGtp.sql 2019-02-10 03:41 1.4K
ensGtp.txt.gz 2019-02-10 03:41 230K
ensPep.sql 2019-02-10 03:41 1.3K
ensPep.txt.gz 2019-02-10 03:41 5.5M
ensemblGeneScaffold.sql 2019-02-10 03:41 1.7K
ensemblSource.sql 2019-02-10 03:41 1.4K
ensemblSource.txt.gz 2019-02-10 03:41 61K
ensemblToGeneName.sql 2019-02-10 03:41 1.4K
ensemblToGeneName.txt.gz 2019-02-10 03:41 121K
ensemblGeneScaffold.txt.gz 2019-02-10 03:41 2.6M
all_mrna.sql 2020-08-19 10:05 2.1K
all_mrna.txt.gz 2020-08-19 10:05 3.1M
mrnaOrientInfo.sql 2020-08-19 10:05 1.8K
mrnaOrientInfo.txt.gz 2020-08-19 10:05 841K
xenoRefGene.sql 2020-08-19 10:11 2.0K
xenoRefGene.txt.gz 2020-08-19 10:11 31M
xenoRefFlat.sql 2020-08-19 10:11 1.7K
xenoRefFlat.txt.gz 2020-08-19 10:11 27M
xenoRefSeqAli.sql 2020-08-19 10:11 2.1K
xenoRefSeqAli.txt.gz 2020-08-19 10:11 29M
gbLoaded.sql 2020-08-19 10:11 1.6K
gbLoaded.txt.gz 2020-08-19 10:11 44K
trackDb_pushedout.sql 2021-12-27 12:20 2.1K
trackDb_pushedout.txt.gz 2021-12-27 12:20 36K
hgFindSpec_pushedout.sql 2021-12-27 12:20 1.8K
hgFindSpec_pushedout.txt.gz 2021-12-27 12:20 798
trackDb.sql 2023-03-28 13:49 2.1K
trackDb.txt.gz 2023-03-28 13:49 38K
hgFindSpec.sql 2023-03-28 13:49 1.8K
hgFindSpec.txt.gz 2023-03-28 13:49 837
tableDescriptions.sql 2024-04-20 02:03 1.5K
tableDescriptions.txt.gz 2024-04-20 02:03 5.5K
tableList.sql 2024-04-21 03:35 1.6K
tableList.txt.gz 2024-04-21 03:35 2.7K
bigFiles.sql 2024-04-21 03:35 1.4K
bigFiles.txt.gz 2024-04-21 03:35 68