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 -
chainPanTro4.sql 2016-10-21 12:53 1.7K
chainPanTro4.txt.gz 2016-10-21 12:53 41M
netPanTro4.sql 2016-10-21 12:53 2.1K
netPanTro4.txt.gz 2016-10-21 12:53 9.3M
chainPanTro4Link.sql 2016-10-21 12:53 1.5K
chainPanTro4Link.txt.gz 2016-10-21 12:54 167M
netPanTro5.sql 2016-10-21 12:54 2.1K
netPanTro5.txt.gz 2016-10-21 12:54 7.7M
chainPanTro5.sql 2016-10-21 12:54 1.7K
chainPanTro5.txt.gz 2016-10-21 12:54 80M
chainPanTro5Link.sql 2016-10-21 12:55 1.5K
chainPanTro5Link.txt.gz 2016-10-21 12:55 244M
chainPanPan2.sql 2017-12-24 07:09 1.7K
chainPanPan2.txt.gz 2017-12-24 07:09 10M
chainPanPan2Link.sql 2017-12-24 07:09 1.5K
chainPanPan2Link.txt.gz 2017-12-24 07:09 109M
netPanPan2.sql 2017-12-24 07:10 2.1K
netPanPan2.txt.gz 2017-12-24 07:10 9.3M
gold.sql 2019-11-19 10:40 1.7K
gold.txt.gz 2019-11-19 10:40 221K
gap.sql 2019-11-19 10:40 1.6K
gap.txt.gz 2019-11-19 10:40 28
gc5BaseBw.sql 2019-11-19 11:59 1.3K
gc5BaseBw.txt.gz 2019-11-19 11:59 66
grp.sql 2019-11-19 12:34 1.4K
grp.txt.gz 2019-11-19 12:34 213
chromInfo.sql 2019-11-19 12:34 1.4K
chromInfo.txt.gz 2019-11-19 12:34 93K
cytoBandIdeo.sql 2019-11-19 12:34 1.5K
cytoBandIdeo.txt.gz 2019-11-19 12:34 91K
cpgIslandExtUnmasked.sql 2019-11-19 13:32 1.7K
cpgIslandExtUnmasked.txt.gz 2019-11-19 13:32 1.1M
simpleRepeat.sql 2019-11-19 17:36 1.9K
simpleRepeat.txt.gz 2019-11-19 17:36 28M
rmsk.sql 2019-11-19 20:10 1.9K
rmsk.txt.gz 2019-11-19 20:10 140M
nestedRepeats.sql 2019-11-19 20:12 2.0K
nestedRepeats.txt.gz 2019-11-19 20:12 18M
windowmaskerSdust.sql 2019-11-19 23:41 1.5K
windowmaskerSdust.txt.gz 2019-11-19 23:41 154M
microsat.sql 2019-11-20 11:02 1.5K
microsat.txt.gz 2019-11-20 11:02 276K
cpgIslandExt.sql 2019-11-20 11:07 1.7K
cpgIslandExt.txt.gz 2019-11-20 11:07 615K
genscan.sql 2019-11-20 12:43 1.7K
genscan.txt.gz 2019-11-20 12:43 2.9M
augustusGene.sql 2019-11-20 14:04 2.0K
augustusGene.txt.gz 2019-11-20 14:04 2.2M
chainHg38.sql 2019-11-21 10:06 1.7K
chainHg38.txt.gz 2019-11-21 10:06 68M
chainHg38Link.sql 2019-11-21 10:07 1.6K
chainHg38Link.txt.gz 2019-11-21 10:07 239M
netHg38.sql 2019-11-21 10:08 2.1K
netHg38.txt.gz 2019-11-21 10:08 6.7M
history.sql 2019-11-27 14:33 1.6K
history.txt.gz 2019-11-27 14:33 517
all_mrna.sql 2019-12-05 11:48 2.1K
all_mrna.txt.gz 2019-12-05 11:48 24K
refSeqAli.sql 2019-12-05 12:00 2.1K
refSeqAli.txt.gz 2019-12-05 12:00 19K
mrnaOrientInfo.sql 2019-12-05 15:40 1.8K
mrnaOrientInfo.txt.gz 2019-12-05 15:40 12K
refGene.sql 2020-08-22 00:57 1.9K
refGene.txt.gz 2020-08-22 00:57 18K
refFlat.sql 2020-08-22 00:57 1.7K
refFlat.txt.gz 2020-08-22 00:57 16K
xenoRefGene.sql 2020-08-22 01:02 2.0K
xenoRefGene.txt.gz 2020-08-22 01:02 33M
xenoRefFlat.sql 2020-08-22 01:02 1.7K
xenoRefFlat.txt.gz 2020-08-22 01:02 31M
xenoRefSeqAli.sql 2020-08-22 01:02 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 01:02 32M
gbLoaded.sql 2020-08-22 01:02 1.6K
gbLoaded.txt.gz 2020-08-22 01:02 38K
trackDb.sql 2023-03-28 13:49 2.1K
trackDb.txt.gz 2023-03-28 13:49 31K
hgFindSpec.sql 2023-03-28 13:49 1.8K
hgFindSpec.txt.gz 2023-03-28 13:49 614
tableDescriptions.sql 2024-12-07 02:03 1.5K
tableDescriptions.txt.gz 2024-12-07 02:03 5.0K
tableList.sql 2024-12-08 03:24 1.6K
tableList.txt.gz 2024-12-08 03:24 2.6K
bigFiles.sql 2024-12-08 03:24 1.4K
bigFiles.txt.gz 2024-12-08 03:24 69