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