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 -
xenoRefSeqAli.txt.gz 2020-05-06 15:36 25M
xenoRefSeqAli.sql 2020-05-06 15:36 2.1K
xenoRefGene.txt.gz 2020-05-06 15:36 23M
xenoRefGene.sql 2020-05-06 15:36 1.9K
xenoRefFlat.txt.gz 2020-05-06 15:36 21M
xenoRefFlat.sql 2020-05-06 15:36 1.7K
windowmaskerSdust.txt.gz 2019-11-19 23:41 143M
windowmaskerSdust.sql 2019-11-19 23:41 1.5K
ucscToRefSeq.txt.gz 2019-11-19 20:41 46K
ucscToRefSeq.sql 2019-11-19 20:41 1.4K
ucscToINSDC.txt.gz 2019-11-19 13:44 49K
ucscToINSDC.sql 2019-11-19 13:44 1.4K
trackDb.txt.gz 2024-01-31 15:13 38K
trackDb.sql 2024-01-31 15:13 2.1K
tableList.txt.gz 2024-11-17 03:14 2.9K
tableList.sql 2024-11-17 03:14 1.6K
tableDescriptions.txt.gz 2024-11-16 02:04 6.1K
tableDescriptions.sql 2024-11-16 02:04 1.4K
simpleRepeat.txt.gz 2019-11-19 17:36 25M
simpleRepeat.sql 2019-11-19 17:36 1.9K
seqNcbiRefSeq.txt.gz 2019-11-20 13:57 947K
seqNcbiRefSeq.sql 2019-11-20 13:57 1.5K
rmsk.txt.gz 2019-11-19 20:10 137M
rmsk.sql 2019-11-19 20:10 1.9K
refSeqAli.txt.gz 2019-12-05 12:00 17K
refSeqAli.sql 2019-12-05 12:00 2.1K
refGene.txt.gz 2020-05-06 15:21 18K
refGene.sql 2020-05-06 15:21 1.9K
refFlat.txt.gz 2020-05-06 15:21 15K
refFlat.sql 2020-05-06 15:21 1.7K
netMm39.txt.gz 2020-11-24 11:11 81M
netMm39.sql 2020-11-24 11:11 2.1K
netMm10.txt.gz 2019-11-21 08:51 81M
netMm10.sql 2019-11-21 08:51 2.1K
netHg38.txt.gz 2019-11-21 10:08 6.2M
netHg38.sql 2019-11-21 10:08 2.1K
nestedRepeats.txt.gz 2019-11-19 20:12 17M
nestedRepeats.sql 2019-11-19 20:12 1.9K
ncbiRefSeqPsl.txt.gz 2019-11-20 12:12 4.3M
ncbiRefSeqPsl.sql 2019-11-20 12:12 2.1K
ncbiRefSeqPredicted.txt.gz 2019-11-20 12:12 3.3M
ncbiRefSeqPredicted.sql 2019-11-20 12:12 2.0K
ncbiRefSeqPepTable.txt.gz 2019-11-20 13:57 9.1M
ncbiRefSeqPepTable.sql 2019-11-20 13:57 1.4K
ncbiRefSeqOther.txt.gz 2019-11-20 13:57 75
ncbiRefSeqOther.sql 2019-11-20 13:57 1.3K
ncbiRefSeqLink.txt.gz 2019-11-20 12:12 1.6M
ncbiRefSeqLink.sql 2019-11-20 12:12 2.0K
ncbiRefSeqCurated.txt.gz 2019-11-20 12:12 17K
ncbiRefSeqCurated.sql 2019-11-20 12:12 2.0K
ncbiRefSeqCds.txt.gz 2019-11-20 13:57 350K
ncbiRefSeqCds.sql 2019-11-20 13:57 1.3K
ncbiRefSeq.txt.gz 2019-11-20 12:12 3.3M
ncbiRefSeq.sql 2019-11-20 12:12 1.9K
mrnaOrientInfo.txt.gz 2019-12-05 15:40 12K
mrnaOrientInfo.sql 2019-12-05 15:40 1.8K
microsat.txt.gz 2019-11-20 11:02 307K
microsat.sql 2019-11-20 11:02 1.5K
history.txt.gz 2019-11-27 14:33 899
history.sql 2019-11-27 14:33 1.6K
hgFindSpec.txt.gz 2024-01-31 15:13 1.1K
hgFindSpec.sql 2024-01-31 15:13 1.8K
grp.txt.gz 2019-11-19 12:34 213
grp.sql 2019-11-19 12:34 1.3K
gold.txt.gz 2019-11-19 10:40 81K
gold.sql 2019-11-19 10:40 1.7K
genscan.txt.gz 2019-11-20 12:43 2.8M
genscan.sql 2019-11-20 12:43 1.7K
gc5BaseBw.txt.gz 2019-11-19 11:59 66
gc5BaseBw.sql 2019-11-19 11:59 1.3K
gap.txt.gz 2019-11-19 10:40 14K
gap.sql 2019-11-19 10:40 1.6K
extNcbiRefSeq.txt.gz 2019-11-20 13:57 91
extNcbiRefSeq.sql 2019-11-20 13:57 1.4K
cytoBandIdeo.txt.gz 2019-11-19 12:34 31K
cytoBandIdeo.sql 2019-11-19 12:34 1.5K
crisprAllTargets.txt.gz 2019-11-27 14:33 69
crisprAllTargets.sql 2019-11-27 14:33 1.3K
cpgIslandExtUnmasked.txt.gz 2019-11-19 13:32 951K
cpgIslandExtUnmasked.sql 2019-11-19 13:32 1.7K
cpgIslandExt.txt.gz 2019-11-20 11:07 579K
cpgIslandExt.sql 2019-11-20 11:07 1.7K
chromInfo.txt.gz 2019-11-19 12:34 34K
chromInfo.sql 2019-11-19 12:34 1.4K
chromAlias.txt.gz 2019-11-19 13:47 56K
chromAlias.sql 2019-11-19 13:47 1.4K
chainMm39Link.txt.gz 2020-11-24 11:07 542M
chainMm39Link.sql 2020-11-24 11:07 1.6K
chainMm39.txt.gz 2020-11-24 11:03 96M
chainMm39.sql 2020-11-24 11:03 1.7K
chainMm10Link.txt.gz 2019-11-21 08:47 567M
chainMm10Link.sql 2019-11-21 08:47 1.5K
chainMm10.txt.gz 2019-11-21 08:43 99M
chainMm10.sql 2019-11-21 08:43 1.7K
chainHg38Link.txt.gz 2019-11-21 10:07 166M
chainHg38Link.sql 2019-11-21 10:07 1.5K
chainHg38.txt.gz 2019-11-21 10:06 48M
chainHg38.sql 2019-11-21 10:06 1.7K
bigFiles.txt.gz 2024-11-17 03:14 119
bigFiles.sql 2024-11-17 03:14 1.4K
augustusGene.txt.gz 2019-11-20 14:04 2.2M
augustusGene.sql 2019-11-20 14:04 1.9K
all_mrna.txt.gz 2019-12-05 11:48 21K
all_mrna.sql 2019-12-05 11:48 2.1K