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 - xenoRefSeqAli.txt.gz 2020-08-22 02:09 43M xenoRefSeqAli.sql 2020-08-22 02:09 2.1K xenoRefGene.txt.gz 2020-08-22 02:09 42M xenoRefGene.sql 2020-08-22 02:09 2.0K xenoRefFlat.txt.gz 2020-08-22 02:09 39M xenoRefFlat.sql 2020-08-22 02:09 1.7K xenoMrna.txt.gz 2020-08-22 01:49 551M xenoMrna.sql 2020-08-22 01:49 2.1K ucscToINSDC.txt.gz 2013-09-15 13:36 351K ucscToINSDC.sql 2013-09-15 13:36 1.4K trackDb_pushedout.txt.gz 2023-09-18 17:06 44K trackDb_pushedout.sql 2023-09-18 17:06 2.1K trackDb.txt.gz 2023-09-19 16:08 44K trackDb.sql 2023-09-19 16:08 2.1K tableList.txt.gz 2024-04-14 03:32 4.0K tableList.sql 2024-04-14 03:32 1.6K tableDescriptions.txt.gz 2024-04-13 02:03 7.1K tableDescriptions.sql 2024-04-13 02:03 1.4K tRNAs.txt.gz 2012-04-23 00:52 11K tRNAs.sql 2012-04-23 00:52 1.7K simpleRepeat.txt.gz 2011-11-22 15:42 25M simpleRepeat.sql 2011-11-22 15:42 1.9K rmsk.txt.gz 2011-11-22 15:46 133M rmsk.sql 2011-11-22 15:45 1.8K phyloP11way.txt.gz 2011-12-11 10:26 80M phyloP11way.sql 2011-12-11 10:26 1.7K phastConsElements11way.txt.gz 2011-12-11 10:24 8.5M phastConsElements11way.sql 2011-12-11 10:23 1.5K phastCons11way.txt.gz 2011-12-11 10:24 73M phastCons11way.sql 2011-12-11 10:24 1.7K netTarSyr2.txt.gz 2015-05-25 02:20 67M netTarSyr2.sql 2015-05-25 02:20 2.1K netRheMac3.txt.gz 2012-12-02 15:14 36M netRheMac3.sql 2012-12-02 15:14 2.1K netPonAbe2.txt.gz 2011-11-22 15:35 22M netPonAbe2.sql 2011-11-22 15:35 2.0K netPapHam1.txt.gz 2012-11-18 15:15 33M netPapHam1.sql 2012-11-18 15:15 2.1K netPanTro3.txt.gz 2011-11-22 15:38 17M netPanTro3.sql 2011-11-22 15:38 2.0K netNomLeu1.txt.gz 2011-11-22 15:35 22M netNomLeu1.sql 2011-11-22 15:35 2.0K netMm10.txt.gz 2012-05-08 06:51 77M netMm10.sql 2012-05-08 06:49 2.0K netMicMur1.txt.gz 2012-11-11 13:03 49M netMicMur1.sql 2012-11-11 13:03 2.1K netHg19.txt.gz 2011-11-22 15:43 15M netHg19.sql 2011-11-22 15:43 2.0K netCalJac3.txt.gz 2011-11-22 15:43 44M netCalJac3.sql 2011-11-22 15:43 2.0K nestedRepeats.txt.gz 2011-11-22 15:39 17M nestedRepeats.sql 2011-11-22 15:39 1.9K multiz11waySummary.txt.gz 2011-12-11 10:24 16M multiz11waySummary.sql 2011-12-11 10:24 1.5K multiz11wayFrames.txt.gz 2011-12-11 10:26 13M multiz11wayFrames.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 mrnaOrientInfo.txt.gz 2019-10-20 08:29 6.0K mrnaOrientInfo.sql 2019-10-20 08:29 1.8K microsat.txt.gz 2015-08-23 17:18 264K microsat.sql 2015-08-23 17:18 1.5K history.txt.gz 2011-11-22 15:39 689 history.sql 2011-11-22 15:39 1.5K hgFindSpec_pushedout.txt.gz 2023-09-18 17:06 900 hgFindSpec_pushedout.sql 2023-09-18 17:06 1.8K hgFindSpec.txt.gz 2023-09-19 16:08 890 hgFindSpec.sql 2023-09-19 16:08 1.8K grp.txt.gz 2014-03-02 04:14 208 grp.sql 2014-03-02 04:14 1.3K gold.txt.gz 2011-11-22 15:35 699K gold.sql 2011-11-22 15:35 1.6K geneid.txt.gz 2015-11-22 16:45 2.9M geneid.sql 2015-11-22 16:45 1.9K gc5BaseBw.txt.gz 2011-11-22 15:39 63 gc5BaseBw.sql 2011-11-22 15:39 1.2K gbLoaded.txt.gz 2020-08-22 02:09 36K gbLoaded.sql 2020-08-22 02:09 1.6K gap.txt.gz 2011-11-22 15:46 5.3M gap.sql 2011-11-22 15:46 1.5K extFile.txt.gz 2011-12-11 10:24 81 extFile.sql 2011-12-11 10:24 1.4K 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 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 ensGene.txt.gz 2018-02-04 07:22 2.6M ensGene.sql 2018-02-04 07:22 1.9K cytoBandIdeo.txt.gz 2013-04-28 15:43 237K cytoBandIdeo.sql 2013-04-28 15:43 1.5K chromInfo.txt.gz 2011-11-22 15:38 226K chromInfo.sql 2011-11-22 15:38 1.3K chromAlias.txt.gz 2016-09-15 17:59 157 chromAlias.sql 2016-09-15 17:59 1.4K chainTarSyr2Link.txt.gz 2015-05-25 02:22 1.0G chainTarSyr2Link.sql 2015-05-25 02:20 1.5K chainTarSyr2.txt.gz 2015-05-25 02:19 252M chainTarSyr2.sql 2015-05-25 02:19 1.7K chainRheMac3Link.txt.gz 2012-12-02 15:12 647M chainRheMac3Link.sql 2012-12-02 15:11 1.6K chainRheMac3.txt.gz 2012-12-02 15:15 217M chainRheMac3.sql 2012-12-02 15:14 1.7K chainPonAbe2Link.txt.gz 2011-11-22 15:44 149M chainPonAbe2Link.sql 2011-11-22 15:44 1.5K chainPonAbe2.txt.gz 2011-11-22 15:35 23M chainPonAbe2.sql 2011-11-22 15:35 1.6K chainPapHam1Link.txt.gz 2012-11-18 15:14 153M chainPapHam1Link.sql 2012-11-18 15:14 1.6K chainPapHam1.txt.gz 2012-11-18 15:15 20M chainPapHam1.sql 2012-11-18 15:15 1.7K chainPanTro3Link.txt.gz 2011-11-22 15:38 106M chainPanTro3Link.sql 2011-11-22 15:38 1.5K chainPanTro3.txt.gz 2011-11-22 15:35 28M chainPanTro3.sql 2011-11-22 15:35 1.6K chainNomLeu1Link.txt.gz 2011-11-22 15:37 123M chainNomLeu1Link.sql 2011-11-22 15:37 1.5K chainNomLeu1.txt.gz 2011-11-22 15:35 15M chainNomLeu1.sql 2011-11-22 15:35 1.6K chainMm10Link.txt.gz 2012-05-08 07:01 514M chainMm10Link.sql 2012-05-08 06:54 1.5K chainMm10.txt.gz 2012-05-08 07:21 83M chainMm10.sql 2012-05-08 07:20 1.6K chainMicMur1Link.txt.gz 2012-11-11 13:03 96M chainMicMur1Link.sql 2012-11-11 13:03 1.6K chainMicMur1.txt.gz 2012-11-11 13:03 7.5M chainMicMur1.sql 2012-11-11 13:03 1.7K chainHg19Link.txt.gz 2011-11-22 15:36 107M chainHg19Link.sql 2011-11-22 15:36 1.5K chainHg19.txt.gz 2011-11-22 15:44 25M chainHg19.sql 2011-11-22 15:44 1.6K chainCalJac3Link.txt.gz 2011-11-22 15:40 218M chainCalJac3Link.sql 2011-11-22 15:39 1.5K chainCalJac3.txt.gz 2011-11-22 15:42 13M chainCalJac3.sql 2011-11-22 15:42 1.6K bigFiles.txt.gz 2024-04-14 03:32 68 bigFiles.sql 2024-04-14 03:32 1.4K augustusGene.txt.gz 2015-07-26 14:02 2.3M augustusGene.sql 2015-07-26 14:02 1.9K all_mrna.txt.gz 2019-10-20 08:29 20K all_mrna.sql 2019-10-20 08:29 2.1K