This directory contains a dump of the UCSC genome annotation database for
the May 2011 (gorGor3.1/gorGor3) assembly of the gorilla genome
(gorGor3, Wellcome Trust Sanger Institute May 2011
(NCBI project 31265, GCA_000151905.1)).
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the Wellcome Trust Sanger Institute.
For more information on the gorilla genome, see the project website:
http://www.sanger.ac.uk/resources/downloads/gorilla/
See also, the WGS records: http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CABD02
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=gorGor3
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/gorGor3/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/gorGor3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/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 gorGor3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql gorGor3 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
------------------------------------------------------------------
Please note the following data sharing guidelines:
http://www.sanger.ac.uk/datasharing/
Name Last modified Size Description
Parent Directory -
bigFiles.txt.gz 2024-11-17 03:36 68
bigFiles.sql 2024-11-17 03:36 1.4K
tableList.txt.gz 2024-11-17 03:36 3.9K
tableList.sql 2024-11-17 03:36 1.6K
tableDescriptions.txt.gz 2024-11-16 02:03 7.1K
tableDescriptions.sql 2024-11-16 02:03 1.4K
hgFindSpec.txt.gz 2024-07-25 09:34 902
hgFindSpec.sql 2024-07-25 09:34 1.8K
trackDb.txt.gz 2024-07-25 09:34 49K
trackDb.sql 2024-07-25 09:34 2.1K
gbLoaded.txt.gz 2020-08-22 02:09 36K
gbLoaded.sql 2020-08-22 02:09 1.6K
xenoRefSeqAli.txt.gz 2020-08-22 02:09 43M
xenoRefSeqAli.sql 2020-08-22 02:09 2.1K
xenoRefFlat.txt.gz 2020-08-22 02:09 39M
xenoRefFlat.sql 2020-08-22 02:09 1.7K
xenoRefGene.txt.gz 2020-08-22 02:09 42M
xenoRefGene.sql 2020-08-22 02:09 2.0K
xenoMrna.txt.gz 2020-08-22 01:49 551M
xenoMrna.sql 2020-08-22 01:49 2.1K
mrnaOrientInfo.txt.gz 2019-10-20 08:29 6.0K
mrnaOrientInfo.sql 2019-10-20 08:29 1.8K
all_mrna.txt.gz 2019-10-20 08:29 20K
all_mrna.sql 2019-10-20 08:29 2.1K
ensemblToGeneName.txt.gz 2018-02-04 07:22 183K
ensemblToGeneName.sql 2018-02-04 07:22 1.4K
ensemblSource.txt.gz 2018-02-04 07:22 96K
ensemblSource.sql 2018-02-04 07:22 1.4K
ensGene.txt.gz 2018-02-04 07:22 2.6M
ensGene.sql 2018-02-04 07:22 1.9K
ensPep.txt.gz 2018-02-04 07:18 8.4M
ensPep.sql 2018-02-04 07:18 1.3K
ensGtp.txt.gz 2018-02-04 07:18 372K
ensGtp.sql 2018-02-04 07:18 1.4K
chromAlias.txt.gz 2016-09-15 17:59 157
chromAlias.sql 2016-09-15 17:59 1.4K
geneid.txt.gz 2015-11-22 16:45 2.9M
geneid.sql 2015-11-22 16:45 1.9K
microsat.txt.gz 2015-08-23 17:18 264K
microsat.sql 2015-08-23 17:18 1.5K
augustusGene.txt.gz 2015-07-26 14:02 2.3M
augustusGene.sql 2015-07-26 14:02 1.9K
chainTarSyr2Link.txt.gz 2015-05-25 02:22 1.0G
chainTarSyr2Link.sql 2015-05-25 02:20 1.5K
netTarSyr2.txt.gz 2015-05-25 02:20 67M
netTarSyr2.sql 2015-05-25 02:20 2.1K
chainTarSyr2.txt.gz 2015-05-25 02:19 252M
chainTarSyr2.sql 2015-05-25 02:19 1.7K
grp.txt.gz 2014-03-02 04:14 208
grp.sql 2014-03-02 04:14 1.3K
ucscToINSDC.txt.gz 2013-09-15 13:36 351K
ucscToINSDC.sql 2013-09-15 13:36 1.4K
cytoBandIdeo.txt.gz 2013-04-28 15:43 237K
cytoBandIdeo.sql 2013-04-28 15:43 1.5K
chainRheMac3.txt.gz 2012-12-02 15:15 217M
chainRheMac3.sql 2012-12-02 15:14 1.7K
netRheMac3.txt.gz 2012-12-02 15:14 36M
netRheMac3.sql 2012-12-02 15:14 2.1K
chainRheMac3Link.txt.gz 2012-12-02 15:12 647M
chainRheMac3Link.sql 2012-12-02 15:11 1.6K
netPapHam1.txt.gz 2012-11-18 15:15 33M
netPapHam1.sql 2012-11-18 15:15 2.1K
chainPapHam1.txt.gz 2012-11-18 15:15 20M
chainPapHam1.sql 2012-11-18 15:15 1.7K
chainPapHam1Link.txt.gz 2012-11-18 15:14 153M
chainPapHam1Link.sql 2012-11-18 15:14 1.6K
chainMicMur1Link.txt.gz 2012-11-11 13:03 96M
chainMicMur1Link.sql 2012-11-11 13:03 1.6K
netMicMur1.txt.gz 2012-11-11 13:03 49M
netMicMur1.sql 2012-11-11 13:03 2.1K
chainMicMur1.txt.gz 2012-11-11 13:03 7.5M
chainMicMur1.sql 2012-11-11 13:03 1.7K
chainMm10.txt.gz 2012-05-08 07:21 83M
chainMm10.sql 2012-05-08 07:20 1.6K
chainMm10Link.txt.gz 2012-05-08 07:01 514M
chainMm10Link.sql 2012-05-08 06:54 1.5K
netMm10.txt.gz 2012-05-08 06:51 77M
netMm10.sql 2012-05-08 06:49 2.0K
tRNAs.txt.gz 2012-04-23 00:52 11K
tRNAs.sql 2012-04-23 00:52 1.7K
multiz11wayFrames.txt.gz 2011-12-11 10:26 13M
multiz11wayFrames.sql 2011-12-11 10:26 1.7K
phyloP11way.txt.gz 2011-12-11 10:26 80M
phyloP11way.sql 2011-12-11 10:26 1.7K
multiz11way.txt.gz 2011-12-11 10:25 178M
multiz11way.sql 2011-12-11 10:24 1.5K
phastCons11way.txt.gz 2011-12-11 10:24 73M
phastCons11way.sql 2011-12-11 10:24 1.7K
extFile.txt.gz 2011-12-11 10:24 81
extFile.sql 2011-12-11 10:24 1.4K
multiz11waySummary.txt.gz 2011-12-11 10:24 16M
multiz11waySummary.sql 2011-12-11 10:24 1.5K
phastConsElements11way.txt.gz 2011-12-11 10:24 8.5M
phastConsElements11way.sql 2011-12-11 10:23 1.5K
gap.txt.gz 2011-11-22 15:46 5.3M
gap.sql 2011-11-22 15:46 1.5K
rmsk.txt.gz 2011-11-22 15:46 133M
rmsk.sql 2011-11-22 15:45 1.8K
chainPonAbe2Link.txt.gz 2011-11-22 15:44 149M
chainPonAbe2Link.sql 2011-11-22 15:44 1.5K
chainHg19.txt.gz 2011-11-22 15:44 25M
chainHg19.sql 2011-11-22 15:44 1.6K
netCalJac3.txt.gz 2011-11-22 15:43 44M
netCalJac3.sql 2011-11-22 15:43 2.0K
netHg19.txt.gz 2011-11-22 15:43 15M
netHg19.sql 2011-11-22 15:43 2.0K
chainCalJac3.txt.gz 2011-11-22 15:42 13M
chainCalJac3.sql 2011-11-22 15:42 1.6K
simpleRepeat.txt.gz 2011-11-22 15:42 25M
simpleRepeat.sql 2011-11-22 15:42 1.9K
chainCalJac3Link.txt.gz 2011-11-22 15:40 218M
chainCalJac3Link.sql 2011-11-22 15:39 1.5K
nestedRepeats.txt.gz 2011-11-22 15:39 17M
nestedRepeats.sql 2011-11-22 15:39 1.9K
history.txt.gz 2011-11-22 15:39 689
history.sql 2011-11-22 15:39 1.5K
gc5BaseBw.txt.gz 2011-11-22 15:39 63
gc5BaseBw.sql 2011-11-22 15:39 1.2K
chainPanTro3Link.txt.gz 2011-11-22 15:38 106M
chainPanTro3Link.sql 2011-11-22 15:38 1.5K
netPanTro3.txt.gz 2011-11-22 15:38 17M
netPanTro3.sql 2011-11-22 15:38 2.0K
chromInfo.txt.gz 2011-11-22 15:38 226K
chromInfo.sql 2011-11-22 15:38 1.3K
chainNomLeu1Link.txt.gz 2011-11-22 15:37 123M
chainNomLeu1Link.sql 2011-11-22 15:37 1.5K
chainHg19Link.txt.gz 2011-11-22 15:36 107M
chainHg19Link.sql 2011-11-22 15:36 1.5K
chainPanTro3.txt.gz 2011-11-22 15:35 28M
chainPanTro3.sql 2011-11-22 15:35 1.6K
netNomLeu1.txt.gz 2011-11-22 15:35 22M
netNomLeu1.sql 2011-11-22 15:35 2.0K
netPonAbe2.txt.gz 2011-11-22 15:35 22M
netPonAbe2.sql 2011-11-22 15:35 2.0K
chainNomLeu1.txt.gz 2011-11-22 15:35 15M
gold.txt.gz 2011-11-22 15:35 699K
gold.sql 2011-11-22 15:35 1.6K
chainNomLeu1.sql 2011-11-22 15:35 1.6K
chainPonAbe2.txt.gz 2011-11-22 15:35 23M
chainPonAbe2.sql 2011-11-22 15:35 1.6K