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 -
all_est.sql 15-May-2016 08:41 2.1K
all_est.txt.gz 15-May-2016 08:41 14M
all_mrna.sql 08-Jan-2017 16:18 2.1K
all_mrna.txt.gz 08-Jan-2017 16:18 3.1M
augustusGene.sql 26-Jul-2015 13:39 1.9K
augustusGene.txt.gz 26-Jul-2015 13:39 3.0M
bigFiles.sql 09-Jul-2017 09:14 1.4K
bigFiles.txt.gz 09-Jul-2017 09:14 68
chainFr3.sql 06-Nov-2012 14:09 1.7K
chainFr3.txt.gz 06-Nov-2012 14:09 20M
chainFr3Link.sql 06-Nov-2012 14:10 1.5K
chainFr3Link.txt.gz 06-Nov-2012 14:10 93M
chainMm10.sql 06-Nov-2012 14:12 1.7K
chainMm10.txt.gz 06-Nov-2012 14:12 7.1M
chainMm10Link.sql 06-Nov-2012 14:11 1.5K
chainMm10Link.txt.gz 06-Nov-2012 14:11 35M
chromInfo.sql 06-Nov-2012 14:10 1.4K
chromInfo.txt.gz 06-Nov-2012 14:10 1.8M
cpgIslandExt.sql 06-Nov-2012 14:10 1.7K
cpgIslandExt.txt.gz 06-Nov-2012 14:10 1.0M
cpgIslandExtUnmasked.sql 01-Jun-2014 13:15 1.7K
cpgIslandExtUnmasked.txt.gz 01-Jun-2014 13:15 1.8M
cytoBandIdeo.sql 28-Apr-2013 15:14 1.5K
cytoBandIdeo.txt.gz 28-Apr-2013 15:14 1.9M
ensGene.sql 14-Sep-2015 01:56 1.9K
ensGene.txt.gz 14-Sep-2015 01:56 2.9M
ensGtp.sql 14-Sep-2015 01:57 1.4K
ensGtp.txt.gz 14-Sep-2015 01:57 230K
ensPep.sql 14-Sep-2015 01:56 1.3K
ensPep.txt.gz 14-Sep-2015 01:56 5.5M
ensemblGeneScaffold.sql 14-Sep-2015 01:57 1.7K
ensemblGeneScaffold.txt.gz 14-Sep-2015 01:57 2.6M
ensemblSource.sql 14-Sep-2015 01:56 1.4K
ensemblSource.txt.gz 14-Sep-2015 01:56 61K
ensemblToGeneName.sql 14-Sep-2015 01:57 1.4K
ensemblToGeneName.txt.gz 14-Sep-2015 01:57 159K
estOrientInfo.sql 15-May-2016 08:41 1.8K
estOrientInfo.txt.gz 15-May-2016 08:41 3.7M
gap.sql 06-Nov-2012 14:11 1.6K
gap.txt.gz 06-Nov-2012 14:11 1.7M
gbLoaded.sql 09-Jul-2017 09:14 1.6K
gbLoaded.txt.gz 09-Jul-2017 09:14 17K
gc5BaseBw.sql 06-Nov-2012 14:11 1.3K
gc5BaseBw.txt.gz 06-Nov-2012 14:11 63
genscan.sql 06-Nov-2012 14:10 1.7K
genscan.txt.gz 06-Nov-2012 14:10 1.9M
gold.sql 06-Nov-2012 14:10 1.7K
gold.txt.gz 06-Nov-2012 14:10 6.1M
grp.sql 02-Mar-2014 03:41 1.3K
grp.txt.gz 02-Mar-2014 03:41 208
hgFindSpec.sql 09-Jul-2017 09:14 1.7K
hgFindSpec.txt.gz 09-Jul-2017 09:14 718
history.sql 06-Nov-2012 14:10 1.6K
history.txt.gz 06-Nov-2012 14:10 551
intronEst.sql 15-May-2016 08:41 2.1K
intronEst.txt.gz 15-May-2016 08:41 4.7M
microsat.sql 23-Aug-2015 16:40 1.5K
microsat.txt.gz 23-Aug-2015 16:40 1.4M
mrnaOrientInfo.sql 08-Jan-2017 16:20 1.8K
mrnaOrientInfo.txt.gz 08-Jan-2017 16:20 840K
nestedRepeats.sql 06-Nov-2012 14:10 1.9K
nestedRepeats.txt.gz 06-Nov-2012 14:10 304K
netFr3.sql 06-Nov-2012 14:10 2.1K
netFr3.txt.gz 06-Nov-2012 14:10 14M
netMm10.sql 06-Nov-2012 14:10 2.1K
netMm10.txt.gz 06-Nov-2012 14:10 5.5M
rmsk.sql 06-Nov-2012 14:11 1.9K
rmsk.txt.gz 06-Nov-2012 14:11 15M
simpleRepeat.sql 06-Nov-2012 14:10 1.9K
simpleRepeat.txt.gz 06-Nov-2012 14:10 21M
tableDescriptions.sql 09-Jul-2017 09:14 1.4K
tableDescriptions.txt.gz 09-Jul-2017 09:14 4.4K
tableList.sql 09-Jul-2017 09:14 1.5K
tableList.txt.gz 09-Jul-2017 09:14 2.5K
trackDb.sql 09-Jul-2017 09:14 2.0K
trackDb.txt.gz 09-Jul-2017 09:14 29K
ucscToEnsembl.sql 11-Aug-2013 03:46 1.4K
ucscToEnsembl.txt.gz 11-Aug-2013 03:46 2.0M
ucscToINSDC.sql 15-Sep-2013 13:09 1.4K
ucscToINSDC.txt.gz 15-Sep-2013 13:09 3.0M
windowmaskerSdust.sql 06-Nov-2012 14:10 1.5K
windowmaskerSdust.txt.gz 06-Nov-2012 14:10 30M
xenoRefFlat.sql 09-Jul-2017 09:14 1.7K
xenoRefFlat.txt.gz 09-Jul-2017 09:14 24M
xenoRefGene.sql 09-Jul-2017 09:14 1.9K
xenoRefGene.txt.gz 09-Jul-2017 09:14 27M
xenoRefSeqAli.sql 09-Jul-2017 09:14 2.1K
xenoRefSeqAli.txt.gz 09-Jul-2017 09:14 22M