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.
---------------------------------------------------------------
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;'
-----------------------------------------------------------------------------
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 -
chainHg38Link.txt.gz 2016-04-13 14:18 166M
windowmaskerSdust.txt.gz 2016-04-13 14:20 148M
rmsk.txt.gz 2016-04-13 14:19 141M
chainHg38.txt.gz 2016-04-13 14:17 58M
simpleRepeat.txt.gz 2016-04-13 14:19 26M
xenoRefGene.txt.gz 2020-08-22 01:27 26M
xenoRefSeqAli.txt.gz 2020-08-22 01:45 24M
xenoRefFlat.txt.gz 2020-08-22 01:27 23M
nestedRepeats.txt.gz 2016-04-13 14:18 18M
ensPep.txt.gz 2021-05-25 14:36 13M
netHg38.txt.gz 2016-04-13 14:18 10M
genscanSubopt.txt.gz 2016-04-13 14:18 5.9M
ensGene.txt.gz 2021-05-25 14:33 3.2M
genscan.txt.gz 2016-04-13 14:19 2.8M
gold.txt.gz 2016-04-13 14:18 2.6M
augustusGene.txt.gz 2016-04-13 14:17 2.5M
gap.txt.gz 2016-04-13 14:19 1.7M
cpgIslandExtUnmasked.txt.gz 2016-04-13 14:18 961K
cpgIslandExt.txt.gz 2016-04-13 14:18 614K
ensGtp.txt.gz 2021-05-25 14:33 555K
chromAlias.txt.gz 2018-02-04 07:23 464K
ucscToRefSeq.txt.gz 2018-02-04 07:23 348K
microsat.txt.gz 2016-04-13 14:17 311K
ucscToINSDC.txt.gz 2018-02-04 07:22 311K
ensemblToGeneName.txt.gz 2021-05-25 14:33 262K
chromInfo.txt.gz 2016-04-13 14:18 201K
cytoBandIdeo.txt.gz 2016-04-13 14:18 200K
ensemblSource.txt.gz 2021-05-25 14:36 154K
gbLoaded.txt.gz 2020-08-22 01:45 42K
trackDb.txt.gz 2024-07-25 09:34 34K
all_mrna.txt.gz 2020-08-22 01:02 24K
refGene.txt.gz 2020-08-22 01:27 18K
refSeqAli.txt.gz 2019-05-26 06:30 17K
refFlat.txt.gz 2020-08-22 01:27 16K
mrnaOrientInfo.txt.gz 2020-08-22 01:02 14K
tableDescriptions.txt.gz 2024-12-28 02:05 6.8K
tableList.txt.gz 2024-12-29 03:05 2.3K
xenoRefSeqAli.sql 2020-08-22 01:45 2.1K
all_mrna.sql 2020-08-22 01:02 2.1K
refSeqAli.sql 2019-05-26 06:30 2.1K
netHg38.sql 2016-04-13 14:18 2.1K
trackDb.sql 2024-07-25 09:34 2.1K
xenoRefGene.sql 2020-08-22 01:27 2.0K
refGene.sql 2020-08-22 01:27 1.9K
ensGene.sql 2021-05-25 14:33 1.9K
augustusGene.sql 2016-04-13 14:17 1.9K
nestedRepeats.sql 2016-04-13 14:18 1.9K
simpleRepeat.sql 2016-04-13 14:19 1.9K
rmsk.sql 2016-04-13 14:19 1.9K
mrnaOrientInfo.sql 2020-08-22 01:02 1.8K
hgFindSpec.sql 2024-07-25 09:34 1.8K
xenoRefFlat.sql 2020-08-22 01:27 1.7K
refFlat.sql 2020-08-22 01:27 1.7K
cpgIslandExtUnmasked.sql 2016-04-13 14:18 1.7K
chainHg38.sql 2016-04-13 14:17 1.7K
cpgIslandExt.sql 2016-04-13 14:18 1.7K
genscan.sql 2016-04-13 14:19 1.7K
gold.sql 2016-04-13 14:18 1.7K
gbLoaded.sql 2020-08-22 01:45 1.6K
gap.sql 2016-04-13 14:19 1.6K
tableList.sql 2024-12-29 03:05 1.6K
history.sql 2016-04-13 14:19 1.6K
genscanSubopt.sql 2016-04-13 14:18 1.6K
chainHg38Link.sql 2016-04-13 14:17 1.5K
cytoBandIdeo.sql 2016-04-13 14:18 1.5K
windowmaskerSdust.sql 2016-04-13 14:20 1.5K
microsat.sql 2016-04-13 14:17 1.5K
tableDescriptions.sql 2024-12-28 02:05 1.5K
ensGtp.sql 2021-05-25 14:33 1.4K
ucscToRefSeq.sql 2018-02-04 07:23 1.4K
ucscToINSDC.sql 2018-02-04 07:22 1.4K
chromAlias.sql 2018-02-04 07:23 1.4K
ensemblToGeneName.sql 2021-05-25 14:33 1.4K
bigFiles.sql 2024-12-29 03:05 1.4K
chromInfo.sql 2016-04-13 14:18 1.4K
ensemblSource.sql 2021-05-25 14:36 1.4K
grp.sql 2016-04-13 14:18 1.3K
ensPep.sql 2021-05-25 14:36 1.3K
gc5BaseBw.sql 2016-04-13 14:19 1.3K
hgFindSpec.txt.gz 2024-07-25 09:34 946
history.txt.gz 2016-04-13 14:19 514
grp.txt.gz 2016-04-13 14:18 213
bigFiles.txt.gz 2024-12-29 03:05 69
gc5BaseBw.txt.gz 2016-04-13 14:19 66