This directory contains a dump of the UCSC genome annotation database for the
Mar. 2016 (GSMRT3/gorGor5) assembly of the gorilla genome
(gorGor5, UNIVERSITY OF WASHINGTON) .
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/705391
http://www.ncbi.nlm.nih.gov/bioproject/PRJEB10880
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=gorGor5
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/gorGor5/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/gorGor5/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/gorGor5/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/gorGor5/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/gorGor5/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 gorGor5 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql gorGor5 --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 -
gap.txt.gz 2019-11-19 10:40 28
gc5BaseBw.txt.gz 2019-11-19 11:59 66
bigFiles.txt.gz 2024-12-08 03:24 69
grp.txt.gz 2019-11-19 12:34 213
history.txt.gz 2019-11-27 14:33 517
hgFindSpec.txt.gz 2023-03-28 13:49 614
gc5BaseBw.sql 2019-11-19 11:59 1.3K
grp.sql 2019-11-19 12:34 1.4K
bigFiles.sql 2024-12-08 03:24 1.4K
chromInfo.sql 2019-11-19 12:34 1.4K
tableDescriptions.sql 2024-12-07 02:03 1.5K
microsat.sql 2019-11-20 11:02 1.5K
windowmaskerSdust.sql 2019-11-19 23:41 1.5K
cytoBandIdeo.sql 2019-11-19 12:34 1.5K
chainPanPan2Link.sql 2017-12-24 07:09 1.5K
chainPanTro4Link.sql 2016-10-21 12:53 1.5K
chainPanTro5Link.sql 2016-10-21 12:55 1.5K
chainHg38Link.sql 2019-11-21 10:07 1.6K
tableList.sql 2024-12-08 03:24 1.6K
history.sql 2019-11-27 14:33 1.6K
gbLoaded.sql 2020-08-22 01:02 1.6K
gap.sql 2019-11-19 10:40 1.6K
gold.sql 2019-11-19 10:40 1.7K
genscan.sql 2019-11-20 12:43 1.7K
cpgIslandExt.sql 2019-11-20 11:07 1.7K
chainPanPan2.sql 2017-12-24 07:09 1.7K
chainPanTro4.sql 2016-10-21 12:53 1.7K
chainPanTro5.sql 2016-10-21 12:54 1.7K
chainHg38.sql 2019-11-21 10:06 1.7K
refFlat.sql 2020-08-22 00:57 1.7K
cpgIslandExtUnmasked.sql 2019-11-19 13:32 1.7K
xenoRefFlat.sql 2020-08-22 01:02 1.7K
hgFindSpec.sql 2023-03-28 13:49 1.8K
mrnaOrientInfo.sql 2019-12-05 15:40 1.8K
rmsk.sql 2019-11-19 20:10 1.9K
refGene.sql 2020-08-22 00:57 1.9K
simpleRepeat.sql 2019-11-19 17:36 1.9K
nestedRepeats.sql 2019-11-19 20:12 2.0K
xenoRefGene.sql 2020-08-22 01:02 2.0K
augustusGene.sql 2019-11-20 14:04 2.0K
trackDb.sql 2023-03-28 13:49 2.1K
netPanPan2.sql 2017-12-24 07:10 2.1K
netPanTro4.sql 2016-10-21 12:53 2.1K
netPanTro5.sql 2016-10-21 12:54 2.1K
netHg38.sql 2019-11-21 10:08 2.1K
all_mrna.sql 2019-12-05 11:48 2.1K
refSeqAli.sql 2019-12-05 12:00 2.1K
xenoRefSeqAli.sql 2020-08-22 01:02 2.1K
tableList.txt.gz 2024-12-08 03:24 2.6K
tableDescriptions.txt.gz 2024-12-07 02:03 5.0K
mrnaOrientInfo.txt.gz 2019-12-05 15:40 12K
refFlat.txt.gz 2020-08-22 00:57 16K
refGene.txt.gz 2020-08-22 00:57 18K
refSeqAli.txt.gz 2019-12-05 12:00 19K
all_mrna.txt.gz 2019-12-05 11:48 24K
trackDb.txt.gz 2023-03-28 13:49 31K
gbLoaded.txt.gz 2020-08-22 01:02 38K
cytoBandIdeo.txt.gz 2019-11-19 12:34 91K
chromInfo.txt.gz 2019-11-19 12:34 93K
gold.txt.gz 2019-11-19 10:40 221K
microsat.txt.gz 2019-11-20 11:02 276K
cpgIslandExt.txt.gz 2019-11-20 11:07 615K
cpgIslandExtUnmasked.txt.gz 2019-11-19 13:32 1.1M
augustusGene.txt.gz 2019-11-20 14:04 2.2M
genscan.txt.gz 2019-11-20 12:43 2.9M
netHg38.txt.gz 2019-11-21 10:08 6.7M
netPanTro5.txt.gz 2016-10-21 12:54 7.7M
netPanTro4.txt.gz 2016-10-21 12:53 9.3M
netPanPan2.txt.gz 2017-12-24 07:10 9.3M
chainPanPan2.txt.gz 2017-12-24 07:09 10M
nestedRepeats.txt.gz 2019-11-19 20:12 18M
simpleRepeat.txt.gz 2019-11-19 17:36 28M
xenoRefFlat.txt.gz 2020-08-22 01:02 31M
xenoRefSeqAli.txt.gz 2020-08-22 01:02 32M
xenoRefGene.txt.gz 2020-08-22 01:02 33M
chainPanTro4.txt.gz 2016-10-21 12:53 41M
chainHg38.txt.gz 2019-11-21 10:06 68M
chainPanTro5.txt.gz 2016-10-21 12:54 80M
chainPanPan2Link.txt.gz 2017-12-24 07:09 109M
rmsk.txt.gz 2019-11-19 20:10 140M
windowmaskerSdust.txt.gz 2019-11-19 23:41 154M
chainPanTro4Link.txt.gz 2016-10-21 12:54 167M
chainHg38Link.txt.gz 2019-11-21 10:07 239M
chainPanTro5Link.txt.gz 2016-10-21 12:55 244M