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 -
chainTarSyr2Link.txt.gz 2015-05-25 02:22 1.0G
chainRheMac3Link.txt.gz 2012-12-02 15:12 647M
xenoMrna.txt.gz 2020-08-22 01:49 551M
chainMm10Link.txt.gz 2012-05-08 07:01 514M
chainTarSyr2.txt.gz 2015-05-25 02:19 252M
chainCalJac3Link.txt.gz 2011-11-22 15:40 218M
chainRheMac3.txt.gz 2012-12-02 15:15 217M
multiz11way.txt.gz 2011-12-11 10:25 178M
chainPapHam1Link.txt.gz 2012-11-18 15:14 153M
chainPonAbe2Link.txt.gz 2011-11-22 15:44 149M
rmsk.txt.gz 2011-11-22 15:46 133M
chainNomLeu1Link.txt.gz 2011-11-22 15:37 123M
chainHg19Link.txt.gz 2011-11-22 15:36 107M
chainPanTro3Link.txt.gz 2011-11-22 15:38 106M
chainMicMur1Link.txt.gz 2012-11-11 13:03 96M
chainMm10.txt.gz 2012-05-08 07:21 83M
phyloP11way.txt.gz 2011-12-11 10:26 80M
netMm10.txt.gz 2012-05-08 06:51 77M
phastCons11way.txt.gz 2011-12-11 10:24 73M
netTarSyr2.txt.gz 2015-05-25 02:20 67M
netMicMur1.txt.gz 2012-11-11 13:03 49M
netCalJac3.txt.gz 2011-11-22 15:43 44M
xenoRefSeqAli.txt.gz 2020-08-22 02:09 43M
xenoRefGene.txt.gz 2020-08-22 02:09 42M
xenoRefFlat.txt.gz 2020-08-22 02:09 39M
netRheMac3.txt.gz 2012-12-02 15:14 36M
netPapHam1.txt.gz 2012-11-18 15:15 33M
chainPanTro3.txt.gz 2011-11-22 15:35 28M
simpleRepeat.txt.gz 2011-11-22 15:42 25M
chainHg19.txt.gz 2011-11-22 15:44 25M
chainPonAbe2.txt.gz 2011-11-22 15:35 23M
netNomLeu1.txt.gz 2011-11-22 15:35 22M
netPonAbe2.txt.gz 2011-11-22 15:35 22M
chainPapHam1.txt.gz 2012-11-18 15:15 20M
nestedRepeats.txt.gz 2011-11-22 15:39 17M
netPanTro3.txt.gz 2011-11-22 15:38 17M
multiz11waySummary.txt.gz 2011-12-11 10:24 16M
chainNomLeu1.txt.gz 2011-11-22 15:35 15M
netHg19.txt.gz 2011-11-22 15:43 15M
chainCalJac3.txt.gz 2011-11-22 15:42 13M
multiz11wayFrames.txt.gz 2011-12-11 10:26 13M
phastConsElements11way.txt.gz 2011-12-11 10:24 8.5M
ensPep.txt.gz 2018-02-04 07:18 8.4M
chainMicMur1.txt.gz 2012-11-11 13:03 7.5M
gap.txt.gz 2011-11-22 15:46 5.3M
geneid.txt.gz 2015-11-22 16:45 2.9M
ensGene.txt.gz 2018-02-04 07:22 2.6M
augustusGene.txt.gz 2015-07-26 14:02 2.3M
gold.txt.gz 2011-11-22 15:35 699K
ensGtp.txt.gz 2018-02-04 07:18 372K
ucscToINSDC.txt.gz 2013-09-15 13:36 351K
microsat.txt.gz 2015-08-23 17:18 264K
cytoBandIdeo.txt.gz 2013-04-28 15:43 237K
chromInfo.txt.gz 2011-11-22 15:38 226K
ensemblToGeneName.txt.gz 2018-02-04 07:22 183K
ensemblSource.txt.gz 2018-02-04 07:22 96K
trackDb.txt.gz 2024-07-25 09:34 49K
gbLoaded.txt.gz 2020-08-22 02:09 36K
all_mrna.txt.gz 2019-10-20 08:29 20K
tRNAs.txt.gz 2012-04-23 00:52 11K
tableDescriptions.txt.gz 2024-11-23 02:03 7.1K
mrnaOrientInfo.txt.gz 2019-10-20 08:29 6.0K
tableList.txt.gz 2024-11-24 03:27 3.9K
xenoRefSeqAli.sql 2020-08-22 02:09 2.1K
xenoMrna.sql 2020-08-22 01:49 2.1K
all_mrna.sql 2019-10-20 08:29 2.1K
netRheMac3.sql 2012-12-02 15:14 2.1K
netPapHam1.sql 2012-11-18 15:15 2.1K
netMicMur1.sql 2012-11-11 13:03 2.1K
netTarSyr2.sql 2015-05-25 02:20 2.1K
trackDb.sql 2024-07-25 09:34 2.1K
netPonAbe2.sql 2011-11-22 15:35 2.0K
netPanTro3.sql 2011-11-22 15:38 2.0K
netNomLeu1.sql 2011-11-22 15:35 2.0K
netCalJac3.sql 2011-11-22 15:43 2.0K
netMm10.sql 2012-05-08 06:49 2.0K
netHg19.sql 2011-11-22 15:43 2.0K
xenoRefGene.sql 2020-08-22 02:09 2.0K
augustusGene.sql 2015-07-26 14:02 1.9K
ensGene.sql 2018-02-04 07:22 1.9K
geneid.sql 2015-11-22 16:45 1.9K
nestedRepeats.sql 2011-11-22 15:39 1.9K
simpleRepeat.sql 2011-11-22 15:42 1.9K
rmsk.sql 2011-11-22 15:45 1.8K
mrnaOrientInfo.sql 2019-10-20 08:29 1.8K
hgFindSpec.sql 2024-07-25 09:34 1.8K
xenoRefFlat.sql 2020-08-22 02:09 1.7K
chainRheMac3.sql 2012-12-02 15:14 1.7K
chainPapHam1.sql 2012-11-18 15:15 1.7K
chainMicMur1.sql 2012-11-11 13:03 1.7K
chainTarSyr2.sql 2015-05-25 02:19 1.7K
phastCons11way.sql 2011-12-11 10:24 1.7K
phyloP11way.sql 2011-12-11 10:26 1.7K
tRNAs.sql 2012-04-23 00:52 1.7K
multiz11wayFrames.sql 2011-12-11 10:26 1.7K
chainPonAbe2.sql 2011-11-22 15:35 1.6K
chainPanTro3.sql 2011-11-22 15:35 1.6K
chainNomLeu1.sql 2011-11-22 15:35 1.6K
chainCalJac3.sql 2011-11-22 15:42 1.6K
chainMm10.sql 2012-05-08 07:20 1.6K
chainHg19.sql 2011-11-22 15:44 1.6K
gbLoaded.sql 2020-08-22 02:09 1.6K
gold.sql 2011-11-22 15:35 1.6K
tableList.sql 2024-11-24 03:27 1.6K
chainRheMac3Link.sql 2012-12-02 15:11 1.6K
chainPapHam1Link.sql 2012-11-18 15:14 1.6K
chainMicMur1Link.sql 2012-11-11 13:03 1.6K
chainTarSyr2Link.sql 2015-05-25 02:20 1.5K
gap.sql 2011-11-22 15:46 1.5K
cytoBandIdeo.sql 2013-04-28 15:43 1.5K
multiz11waySummary.sql 2011-12-11 10:24 1.5K
history.sql 2011-11-22 15:39 1.5K
phastConsElements11way.sql 2011-12-11 10:23 1.5K
microsat.sql 2015-08-23 17:18 1.5K
chainPonAbe2Link.sql 2011-11-22 15:44 1.5K
chainPanTro3Link.sql 2011-11-22 15:38 1.5K
chainNomLeu1Link.sql 2011-11-22 15:37 1.5K
chainCalJac3Link.sql 2011-11-22 15:39 1.5K
chainMm10Link.sql 2012-05-08 06:54 1.5K
chainHg19Link.sql 2011-11-22 15:36 1.5K
multiz11way.sql 2011-12-11 10:24 1.5K
chromAlias.sql 2016-09-15 17:59 1.4K
ucscToINSDC.sql 2013-09-15 13:36 1.4K
tableDescriptions.sql 2024-11-23 02:03 1.4K
ensGtp.sql 2018-02-04 07:18 1.4K
ensemblToGeneName.sql 2018-02-04 07:22 1.4K
bigFiles.sql 2024-11-24 03:27 1.4K
ensemblSource.sql 2018-02-04 07:22 1.4K
extFile.sql 2011-12-11 10:24 1.4K
grp.sql 2014-03-02 04:14 1.3K
ensPep.sql 2018-02-04 07:18 1.3K
chromInfo.sql 2011-11-22 15:38 1.3K
gc5BaseBw.sql 2011-11-22 15:39 1.2K
hgFindSpec.txt.gz 2024-07-25 09:34 902
history.txt.gz 2011-11-22 15:39 689
grp.txt.gz 2014-03-02 04:14 208
chromAlias.txt.gz 2016-09-15 17:59 157
extFile.txt.gz 2011-12-11 10:24 81
bigFiles.txt.gz 2024-11-24 03:27 68
gc5BaseBw.txt.gz 2011-11-22 15:39 63