This directory contains a dump of the UCSC genome annotation database for the
    Dec 2014 (gorGor4.1/gorGor4) assembly of the gorilla genome
    (gorGor4, Wellcome Trust Sanger Institute Dec 2014 (NCBI project 31265, GCA_000151905.1)) .

The annotations were generated by UCSC and collaborators worldwide.

For more information about this assembly, please note the NCBI resources:
    http://www.ncbi.nlm.nih.gov/genome/2156
    http://www.ncbi.nlm.nih.gov/genome/assembly/503571
    http://www.ncbi.nlm.nih.gov/bioproject/31265

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=gorGor4
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.cse.ucsc.edu, then go to
the directory goldenPath/gorGor4/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/gorGor4/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/gorGor4/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/gorGor4/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/gorGor4/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 gorGor4 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql gorGor4 --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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.

      Name                        Last modified      Size  Description
Parent Directory - xenoRefSeqAli.txt.gz 2020-08-22 01:45 24M xenoRefSeqAli.sql 2020-08-22 01:45 2.1K xenoRefGene.txt.gz 2020-08-22 01:27 26M xenoRefGene.sql 2020-08-22 01:27 1.9K xenoRefFlat.txt.gz 2020-08-22 01:27 23M xenoRefFlat.sql 2020-08-22 01:27 1.7K windowmaskerSdust.txt.gz 2016-04-13 14:20 148M windowmaskerSdust.sql 2016-04-13 14:20 1.5K ucscToRefSeq.txt.gz 2018-02-04 07:23 348K ucscToRefSeq.sql 2018-02-04 07:23 1.4K ucscToINSDC.txt.gz 2018-02-04 07:22 311K ucscToINSDC.sql 2018-02-04 07:22 1.4K trackDb.txt.gz 2021-12-27 12:23 21K trackDb.sql 2021-12-27 12:23 2.1K tableList.txt.gz 2022-08-07 03:03 2.3K tableList.sql 2022-08-07 03:03 1.6K tableDescriptions.txt.gz 2019-07-21 03:41 6.8K tableDescriptions.sql 2019-07-21 03:41 1.4K simpleRepeat.txt.gz 2016-04-13 14:19 26M simpleRepeat.sql 2016-04-13 14:19 1.9K rmsk.txt.gz 2016-04-13 14:19 141M rmsk.sql 2016-04-13 14:19 1.9K refSeqAli.txt.gz 2019-05-26 06:30 17K refSeqAli.sql 2019-05-26 06:30 2.1K refGene.txt.gz 2020-08-22 01:27 18K refGene.sql 2020-08-22 01:27 1.9K refFlat.txt.gz 2020-08-22 01:27 16K refFlat.sql 2020-08-22 01:27 1.7K netHg38.txt.gz 2016-04-13 14:18 10M netHg38.sql 2016-04-13 14:18 2.1K nestedRepeats.txt.gz 2016-04-13 14:18 18M nestedRepeats.sql 2016-04-13 14:18 1.9K mrnaOrientInfo.txt.gz 2020-08-22 01:02 14K mrnaOrientInfo.sql 2020-08-22 01:02 1.8K microsat.txt.gz 2016-04-13 14:17 311K microsat.sql 2016-04-13 14:17 1.5K history.txt.gz 2016-04-13 14:19 514 history.sql 2016-04-13 14:19 1.6K hgFindSpec.txt.gz 2021-12-27 12:23 837 hgFindSpec.sql 2021-12-27 12:23 1.8K grp.txt.gz 2016-04-13 14:18 213 grp.sql 2016-04-13 14:18 1.3K gold.txt.gz 2016-04-13 14:18 2.6M gold.sql 2016-04-13 14:18 1.7K genscanSubopt.txt.gz 2016-04-13 14:18 5.9M genscanSubopt.sql 2016-04-13 14:18 1.6K genscan.txt.gz 2016-04-13 14:19 2.8M genscan.sql 2016-04-13 14:19 1.7K gc5BaseBw.txt.gz 2016-04-13 14:19 66 gc5BaseBw.sql 2016-04-13 14:19 1.3K gbLoaded.txt.gz 2020-08-22 01:45 42K gbLoaded.sql 2020-08-22 01:45 1.6K gap.txt.gz 2016-04-13 14:19 1.7M gap.sql 2016-04-13 14:19 1.6K ensemblToGeneName.txt.gz 2021-05-25 14:33 262K ensemblToGeneName.sql 2021-05-25 14:33 1.4K ensemblSource.txt.gz 2021-05-25 14:36 154K ensemblSource.sql 2021-05-25 14:36 1.4K ensPep.txt.gz 2021-05-25 14:36 13M ensPep.sql 2021-05-25 14:36 1.3K ensGtp.txt.gz 2021-05-25 14:33 555K ensGtp.sql 2021-05-25 14:33 1.4K ensGene.txt.gz 2021-05-25 14:33 3.2M ensGene.sql 2021-05-25 14:33 1.9K cytoBandIdeo.txt.gz 2016-04-13 14:18 200K cytoBandIdeo.sql 2016-04-13 14:18 1.5K cpgIslandExtUnmasked.txt.gz 2016-04-13 14:18 961K cpgIslandExtUnmasked.sql 2016-04-13 14:18 1.7K cpgIslandExt.txt.gz 2016-04-13 14:18 614K cpgIslandExt.sql 2016-04-13 14:18 1.7K chromInfo.txt.gz 2016-04-13 14:18 201K chromInfo.sql 2016-04-13 14:18 1.4K chromAlias.txt.gz 2018-02-04 07:23 464K chromAlias.sql 2018-02-04 07:23 1.4K chainHg38Link.txt.gz 2016-04-13 14:18 166M chainHg38Link.sql 2016-04-13 14:17 1.5K chainHg38.txt.gz 2016-04-13 14:17 58M chainHg38.sql 2016-04-13 14:17 1.7K bigFiles.txt.gz 2022-08-07 03:03 69 bigFiles.sql 2022-08-07 03:03 1.4K augustusGene.txt.gz 2016-04-13 14:17 2.5M augustusGene.sql 2016-04-13 14:17 1.9K all_mrna.txt.gz 2020-08-22 01:02 24K all_mrna.sql 2020-08-22 01:02 2.1K