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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
xenoRefSeqAli.txt.gz 2020-08-22 01:45 24M
xenoRefSeqAli.sql 2020-08-22 01:45 2.1K
xenoRefGene.txt.gz 2020-08-22 01:27 26M
xenoRefGene.sql 2020-08-22 01:27 2.0K
xenoRefFlat.txt.gz 2020-08-22 01:27 23M
xenoRefFlat.sql 2020-08-22 01:27 1.7K
windowmaskerSdust.txt.gz 2016-04-13 14:20 148M
windowmaskerSdust.sql 2016-04-13 14:20 1.5K
ucscToRefSeq.txt.gz 2018-02-04 07:23 348K
ucscToRefSeq.sql 2018-02-04 07:23 1.4K
ucscToINSDC.txt.gz 2018-02-04 07:22 311K
ucscToINSDC.sql 2018-02-04 07:22 1.4K
trackDb.txt.gz 2024-07-25 09:34 34K
trackDb.sql 2024-07-25 09:34 2.1K
tableList.txt.gz 2024-11-24 03:06 2.3K
tableList.sql 2024-11-24 03:06 1.6K
tableDescriptions.txt.gz 2024-11-23 02:03 6.8K
tableDescriptions.sql 2024-11-23 02:03 1.4K
simpleRepeat.txt.gz 2016-04-13 14:19 26M
simpleRepeat.sql 2016-04-13 14:19 1.9K
rmsk.txt.gz 2016-04-13 14:19 141M
rmsk.sql 2016-04-13 14:19 1.9K
refSeqAli.txt.gz 2019-05-26 06:30 17K
refSeqAli.sql 2019-05-26 06:30 2.1K
refGene.txt.gz 2020-08-22 01:27 18K
refGene.sql 2020-08-22 01:27 1.9K
refFlat.txt.gz 2020-08-22 01:27 16K
refFlat.sql 2020-08-22 01:27 1.7K
netHg38.txt.gz 2016-04-13 14:18 10M
netHg38.sql 2016-04-13 14:18 2.1K
nestedRepeats.txt.gz 2016-04-13 14:18 18M
nestedRepeats.sql 2016-04-13 14:18 1.9K
mrnaOrientInfo.txt.gz 2020-08-22 01:02 14K
mrnaOrientInfo.sql 2020-08-22 01:02 1.8K
microsat.txt.gz 2016-04-13 14:17 311K
microsat.sql 2016-04-13 14:17 1.5K
history.txt.gz 2016-04-13 14:19 514
history.sql 2016-04-13 14:19 1.6K
hgFindSpec.txt.gz 2024-07-25 09:34 946
hgFindSpec.sql 2024-07-25 09:34 1.8K
grp.txt.gz 2016-04-13 14:18 213
grp.sql 2016-04-13 14:18 1.3K
gold.txt.gz 2016-04-13 14:18 2.6M
gold.sql 2016-04-13 14:18 1.7K
genscanSubopt.txt.gz 2016-04-13 14:18 5.9M
genscanSubopt.sql 2016-04-13 14:18 1.6K
genscan.txt.gz 2016-04-13 14:19 2.8M
genscan.sql 2016-04-13 14:19 1.7K
gc5BaseBw.txt.gz 2016-04-13 14:19 66
gc5BaseBw.sql 2016-04-13 14:19 1.3K
gbLoaded.txt.gz 2020-08-22 01:45 42K
gbLoaded.sql 2020-08-22 01:45 1.6K
gap.txt.gz 2016-04-13 14:19 1.7M
gap.sql 2016-04-13 14:19 1.6K
ensemblToGeneName.txt.gz 2021-05-25 14:33 262K
ensemblToGeneName.sql 2021-05-25 14:33 1.4K
ensemblSource.txt.gz 2021-05-25 14:36 154K
ensemblSource.sql 2021-05-25 14:36 1.4K
ensPep.txt.gz 2021-05-25 14:36 13M
ensPep.sql 2021-05-25 14:36 1.3K
ensGtp.txt.gz 2021-05-25 14:33 555K
ensGtp.sql 2021-05-25 14:33 1.4K
ensGene.txt.gz 2021-05-25 14:33 3.2M
ensGene.sql 2021-05-25 14:33 1.9K
cytoBandIdeo.txt.gz 2016-04-13 14:18 200K
cytoBandIdeo.sql 2016-04-13 14:18 1.5K
cpgIslandExtUnmasked.txt.gz 2016-04-13 14:18 961K
cpgIslandExtUnmasked.sql 2016-04-13 14:18 1.7K
cpgIslandExt.txt.gz 2016-04-13 14:18 614K
cpgIslandExt.sql 2016-04-13 14:18 1.7K
chromInfo.txt.gz 2016-04-13 14:18 201K
chromInfo.sql 2016-04-13 14:18 1.4K
chromAlias.txt.gz 2018-02-04 07:23 464K
chromAlias.sql 2018-02-04 07:23 1.4K
chainHg38Link.txt.gz 2016-04-13 14:18 166M
chainHg38Link.sql 2016-04-13 14:17 1.5K
chainHg38.txt.gz 2016-04-13 14:17 58M
chainHg38.sql 2016-04-13 14:17 1.7K
bigFiles.txt.gz 2024-11-24 03:06 69
bigFiles.sql 2024-11-24 03:06 1.4K
augustusGene.txt.gz 2016-04-13 14:17 2.5M
augustusGene.sql 2016-04-13 14:17 1.9K
all_mrna.txt.gz 2020-08-22 01:02 24K
all_mrna.sql 2020-08-22 01:02 2.1K