This directory contains a dump of the UCSC genome annotation database for the
Aug. 2019 (Kamilah_GGO_v0/gorGor6) assembly of the gorilla genome
(gorGor6, University of Washington) .
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
https://www.ncbi.nlm.nih.gov/genome/2156
https://www.ncbi.nlm.nih.gov/genome/assembly/4439481
https://www.ncbi.nlm.nih.gov/bioproject/369439
https://www.ncbi.nlm.nih.gov/biosample/SAMN11078986
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=gorGor6
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.soe.ucsc.edu, then go to
the directory goldenPath/gorGor6/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.soe.ucsc.edu/goldenPath/gorGor6/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/database/gc5Base.txt.gz'
-O gc5Base.txt.gz
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 gorGor6 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql gorGor6 --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 -
gc5BaseBw.txt.gz 2019-11-19 11:59 66
crisprAllTargets.txt.gz 2019-11-27 14:33 69
ncbiRefSeqOther.txt.gz 2019-11-20 13:57 75
extNcbiRefSeq.txt.gz 2019-11-20 13:57 91
bigFiles.txt.gz 2024-04-14 03:05 119
grp.txt.gz 2019-11-19 12:34 213
history.txt.gz 2019-11-27 14:33 899
hgFindSpec.txt.gz 2024-01-31 15:13 1.1K
hgFindSpec_pushedout.txt.gz 2024-01-31 15:13 1.1K
gc5BaseBw.sql 2019-11-19 11:59 1.3K
ncbiRefSeqOther.sql 2019-11-20 13:57 1.3K
crisprAllTargets.sql 2019-11-27 14:33 1.3K
ncbiRefSeqCds.sql 2019-11-20 13:57 1.3K
grp.sql 2019-11-19 12:34 1.3K
ncbiRefSeqPepTable.sql 2019-11-20 13:57 1.4K
chromInfo.sql 2019-11-19 12:34 1.4K
bigFiles.sql 2024-04-14 03:05 1.4K
chromAlias.sql 2019-11-19 13:47 1.4K
ucscToINSDC.sql 2019-11-19 13:44 1.4K
ucscToRefSeq.sql 2019-11-19 20:41 1.4K
extNcbiRefSeq.sql 2019-11-20 13:57 1.4K
tableDescriptions.sql 2024-04-13 02:04 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
chainHg38Link.sql 2019-11-21 10:07 1.5K
chainMm10Link.sql 2019-11-21 08:47 1.5K
seqNcbiRefSeq.sql 2019-11-20 13:57 1.5K
chainMm39Link.sql 2020-11-24 11:07 1.6K
history.sql 2019-11-27 14:33 1.6K
tableList.sql 2024-04-14 03:05 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
chainHg38.sql 2019-11-21 10:06 1.7K
chainMm10.sql 2019-11-21 08:43 1.7K
refFlat.sql 2020-05-06 15:21 1.7K
cpgIslandExtUnmasked.sql 2019-11-19 13:32 1.7K
xenoRefFlat.sql 2020-05-06 15:36 1.7K
chainMm39.sql 2020-11-24 11:03 1.7K
hgFindSpec.sql 2024-01-31 15:13 1.8K
mrnaOrientInfo.sql 2019-12-05 15:40 1.8K
hgFindSpec_pushedout.sql 2024-01-31 15:13 1.8K
rmsk.sql 2019-11-19 20:10 1.9K
refGene.sql 2020-05-06 15:21 1.9K
simpleRepeat.sql 2019-11-19 17:36 1.9K
ncbiRefSeq.sql 2019-11-20 12:12 1.9K
nestedRepeats.sql 2019-11-19 20:12 1.9K
xenoRefGene.sql 2020-05-06 15:36 1.9K
augustusGene.sql 2019-11-20 14:04 1.9K
ncbiRefSeqCurated.sql 2019-11-20 12:12 2.0K
ncbiRefSeqPredicted.sql 2019-11-20 12:12 2.0K
ncbiRefSeqLink.sql 2019-11-20 12:12 2.0K
trackDb.sql 2024-01-31 15:13 2.1K
trackDb_pushedout.sql 2024-01-31 15:13 2.1K
netHg38.sql 2019-11-21 10:08 2.1K
netMm10.sql 2019-11-21 08:51 2.1K
all_mrna.sql 2019-12-05 11:48 2.1K
refSeqAli.sql 2019-12-05 12:00 2.1K
netMm39.sql 2020-11-24 11:11 2.1K
ncbiRefSeqPsl.sql 2019-11-20 12:12 2.1K
xenoRefSeqAli.sql 2020-05-06 15:36 2.1K
tableList.txt.gz 2024-04-14 03:05 3.1K
tableDescriptions.txt.gz 2024-04-13 02:04 6.1K
mrnaOrientInfo.txt.gz 2019-12-05 15:40 12K
gap.txt.gz 2019-11-19 10:40 14K
refFlat.txt.gz 2020-05-06 15:21 15K
refSeqAli.txt.gz 2019-12-05 12:00 17K
ncbiRefSeqCurated.txt.gz 2019-11-20 12:12 17K
refGene.txt.gz 2020-05-06 15:21 18K
all_mrna.txt.gz 2019-12-05 11:48 21K
cytoBandIdeo.txt.gz 2019-11-19 12:34 31K
chromInfo.txt.gz 2019-11-19 12:34 34K
trackDb.txt.gz 2024-01-31 15:13 38K
trackDb_pushedout.txt.gz 2024-01-31 15:13 38K
ucscToRefSeq.txt.gz 2019-11-19 20:41 46K
ucscToINSDC.txt.gz 2019-11-19 13:44 49K
chromAlias.txt.gz 2019-11-19 13:47 56K
gold.txt.gz 2019-11-19 10:40 81K
microsat.txt.gz 2019-11-20 11:02 307K
ncbiRefSeqCds.txt.gz 2019-11-20 13:57 350K
cpgIslandExt.txt.gz 2019-11-20 11:07 579K
seqNcbiRefSeq.txt.gz 2019-11-20 13:57 947K
cpgIslandExtUnmasked.txt.gz 2019-11-19 13:32 951K
ncbiRefSeqLink.txt.gz 2019-11-20 12:12 1.6M
augustusGene.txt.gz 2019-11-20 14:04 2.2M
genscan.txt.gz 2019-11-20 12:43 2.8M
ncbiRefSeqPredicted.txt.gz 2019-11-20 12:12 3.3M
ncbiRefSeq.txt.gz 2019-11-20 12:12 3.3M
ncbiRefSeqPsl.txt.gz 2019-11-20 12:12 4.3M
netHg38.txt.gz 2019-11-21 10:08 6.2M
ncbiRefSeqPepTable.txt.gz 2019-11-20 13:57 9.1M
nestedRepeats.txt.gz 2019-11-19 20:12 17M
xenoRefFlat.txt.gz 2020-05-06 15:36 21M
xenoRefGene.txt.gz 2020-05-06 15:36 23M
xenoRefSeqAli.txt.gz 2020-05-06 15:36 25M
simpleRepeat.txt.gz 2019-11-19 17:36 25M
chainHg38.txt.gz 2019-11-21 10:06 48M
netMm10.txt.gz 2019-11-21 08:51 81M
netMm39.txt.gz 2020-11-24 11:11 81M
chainMm39.txt.gz 2020-11-24 11:03 96M
chainMm10.txt.gz 2019-11-21 08:43 99M
rmsk.txt.gz 2019-11-19 20:10 137M
windowmaskerSdust.txt.gz 2019-11-19 23:41 143M
chainHg38Link.txt.gz 2019-11-21 10:07 166M
chainMm39Link.txt.gz 2020-11-24 11:07 542M
chainMm10Link.txt.gz 2019-11-21 08:47 567M