This directory contains a dump of the UCSC genome annotation database for the
Dec 2014 (gorGor4.1/gorGor4) assembly of the gorilla genome
(gorGor4, Wellcome Trust Sanger Institute Dec 2014 (NCBI project 31265, GCA_000151905.1)) .
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/2156
http://www.ncbi.nlm.nih.gov/genome/assembly/503571
http://www.ncbi.nlm.nih.gov/bioproject/31265
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=gorGor4
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/gorGor4/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/gorGor4/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/gorGor4/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/gorGor4/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/gorGor4/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 gorGor4 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql gorGor4 --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.
Name Last modified Size Description
Parent Directory -
all_mrna.sql 2020-08-22 01:02 2.1K
all_mrna.txt.gz 2020-08-22 01:02 24K
augustusGene.sql 2016-04-13 14:17 1.9K
augustusGene.txt.gz 2016-04-13 14:17 2.5M
bigFiles.sql 2024-11-17 03:16 1.4K
bigFiles.txt.gz 2024-11-17 03:16 69
chainHg38.sql 2016-04-13 14:17 1.7K
chainHg38.txt.gz 2016-04-13 14:17 58M
chainHg38Link.sql 2016-04-13 14:17 1.5K
chainHg38Link.txt.gz 2016-04-13 14:18 166M
chromAlias.sql 2018-02-04 07:23 1.4K
chromAlias.txt.gz 2018-02-04 07:23 464K
chromInfo.sql 2016-04-13 14:18 1.4K
chromInfo.txt.gz 2016-04-13 14:18 201K
cpgIslandExt.sql 2016-04-13 14:18 1.7K
cpgIslandExt.txt.gz 2016-04-13 14:18 614K
cpgIslandExtUnmasked.sql 2016-04-13 14:18 1.7K
cpgIslandExtUnmasked.txt.gz 2016-04-13 14:18 961K
cytoBandIdeo.sql 2016-04-13 14:18 1.5K
cytoBandIdeo.txt.gz 2016-04-13 14:18 200K
ensGene.sql 2021-05-25 14:33 1.9K
ensGene.txt.gz 2021-05-25 14:33 3.2M
ensGtp.sql 2021-05-25 14:33 1.4K
ensGtp.txt.gz 2021-05-25 14:33 555K
ensPep.sql 2021-05-25 14:36 1.3K
ensPep.txt.gz 2021-05-25 14:36 13M
ensemblSource.sql 2021-05-25 14:36 1.4K
ensemblSource.txt.gz 2021-05-25 14:36 154K
ensemblToGeneName.sql 2021-05-25 14:33 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:33 262K
gap.sql 2016-04-13 14:19 1.6K
gap.txt.gz 2016-04-13 14:19 1.7M
gbLoaded.sql 2020-08-22 01:45 1.6K
gbLoaded.txt.gz 2020-08-22 01:45 42K
gc5BaseBw.sql 2016-04-13 14:19 1.3K
gc5BaseBw.txt.gz 2016-04-13 14:19 66
genscan.sql 2016-04-13 14:19 1.7K
genscan.txt.gz 2016-04-13 14:19 2.8M
genscanSubopt.sql 2016-04-13 14:18 1.6K
genscanSubopt.txt.gz 2016-04-13 14:18 5.9M
gold.sql 2016-04-13 14:18 1.7K
gold.txt.gz 2016-04-13 14:18 2.6M
grp.sql 2016-04-13 14:18 1.3K
grp.txt.gz 2016-04-13 14:18 213
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 946
history.sql 2016-04-13 14:19 1.6K
history.txt.gz 2016-04-13 14:19 514
microsat.sql 2016-04-13 14:17 1.5K
microsat.txt.gz 2016-04-13 14:17 311K
mrnaOrientInfo.sql 2020-08-22 01:02 1.8K
mrnaOrientInfo.txt.gz 2020-08-22 01:02 14K
nestedRepeats.sql 2016-04-13 14:18 1.9K
nestedRepeats.txt.gz 2016-04-13 14:18 18M
netHg38.sql 2016-04-13 14:18 2.1K
netHg38.txt.gz 2016-04-13 14:18 10M
refFlat.sql 2020-08-22 01:27 1.7K
refFlat.txt.gz 2020-08-22 01:27 16K
refGene.sql 2020-08-22 01:27 1.9K
refGene.txt.gz 2020-08-22 01:27 18K
refSeqAli.sql 2019-05-26 06:30 2.1K
refSeqAli.txt.gz 2019-05-26 06:30 17K
rmsk.sql 2016-04-13 14:19 1.9K
rmsk.txt.gz 2016-04-13 14:19 141M
simpleRepeat.sql 2016-04-13 14:19 1.9K
simpleRepeat.txt.gz 2016-04-13 14:19 26M
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 6.8K
tableList.sql 2024-11-17 03:16 1.6K
tableList.txt.gz 2024-11-17 03:16 2.3K
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 34K
ucscToINSDC.sql 2018-02-04 07:22 1.4K
ucscToINSDC.txt.gz 2018-02-04 07:22 311K
ucscToRefSeq.sql 2018-02-04 07:23 1.4K
ucscToRefSeq.txt.gz 2018-02-04 07:23 348K
windowmaskerSdust.sql 2016-04-13 14:20 1.5K
windowmaskerSdust.txt.gz 2016-04-13 14:20 148M
xenoRefFlat.sql 2020-08-22 01:27 1.7K
xenoRefFlat.txt.gz 2020-08-22 01:27 23M
xenoRefGene.sql 2020-08-22 01:27 2.0K
xenoRefGene.txt.gz 2020-08-22 01:27 26M
xenoRefSeqAli.sql 2020-08-22 01:45 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 01:45 24M