This directory contains a dump of the UCSC genome annotation database for the
    Mar. 2016 (GSMRT3/gorGor5) assembly of the gorilla genome
    (gorGor5, UNIVERSITY OF WASHINGTON) .

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/705391
    http://www.ncbi.nlm.nih.gov/bioproject/PRJEB10880

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=gorGor5
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/gorGor5/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/gorGor5/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/gorGor5/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/gorGor5/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/gorGor5/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 gorGor5 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql gorGor5 --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 01:02 32M xenoRefSeqAli.sql 2020-08-22 01:02 2.1K xenoRefGene.txt.gz 2020-08-22 01:02 33M xenoRefGene.sql 2020-08-22 01:02 2.0K xenoRefFlat.txt.gz 2020-08-22 01:02 31M xenoRefFlat.sql 2020-08-22 01:02 1.7K windowmaskerSdust.txt.gz 2019-11-19 23:41 154M windowmaskerSdust.sql 2019-11-19 23:41 1.5K trackDb_pushedout.txt.gz 2021-08-02 14:29 30K trackDb_pushedout.sql 2021-08-02 14:29 2.1K trackDb.txt.gz 2023-03-28 13:49 31K trackDb.sql 2023-03-28 13:49 2.1K tableList.txt.gz 2024-03-24 03:33 2.7K tableList.sql 2024-03-24 03:33 1.6K tableDescriptions.txt.gz 2024-03-23 02:03 5.0K tableDescriptions.sql 2024-03-23 02:03 1.4K simpleRepeat.txt.gz 2019-11-19 17:36 28M simpleRepeat.sql 2019-11-19 17:36 1.9K rmsk.txt.gz 2019-11-19 20:10 140M rmsk.sql 2019-11-19 20:10 1.9K refSeqAli.txt.gz 2019-12-05 12:00 19K refSeqAli.sql 2019-12-05 12:00 2.1K refGene.txt.gz 2020-08-22 00:57 18K refGene.sql 2020-08-22 00:57 1.9K refFlat.txt.gz 2020-08-22 00:57 16K refFlat.sql 2020-08-22 00:57 1.7K netPanTro5.txt.gz 2016-10-21 12:54 7.7M netPanTro5.sql 2016-10-21 12:54 2.1K netPanTro4.txt.gz 2016-10-21 12:53 9.3M netPanTro4.sql 2016-10-21 12:53 2.1K netPanPan2.txt.gz 2017-12-24 07:10 9.3M netPanPan2.sql 2017-12-24 07:10 2.1K netHg38.txt.gz 2019-11-21 10:08 6.7M netHg38.sql 2019-11-21 10:08 2.1K nestedRepeats.txt.gz 2019-11-19 20:12 18M nestedRepeats.sql 2019-11-19 20:12 2.0K mrnaOrientInfo.txt.gz 2019-12-05 15:40 12K mrnaOrientInfo.sql 2019-12-05 15:40 1.8K microsat.txt.gz 2019-11-20 11:02 276K microsat.sql 2019-11-20 11:02 1.5K history.txt.gz 2019-11-27 14:33 517 history.sql 2019-11-27 14:33 1.6K hgFindSpec_pushedout.txt.gz 2021-08-02 14:29 577 hgFindSpec_pushedout.sql 2021-08-02 14:29 1.8K hgFindSpec.txt.gz 2023-03-28 13:49 614 hgFindSpec.sql 2023-03-28 13:49 1.8K grp.txt.gz 2019-11-19 12:34 213 grp.sql 2019-11-19 12:34 1.4K gold.txt.gz 2019-11-19 10:40 221K gold.sql 2019-11-19 10:40 1.7K genscan.txt.gz 2019-11-20 12:43 2.9M genscan.sql 2019-11-20 12:43 1.7K gc5BaseBw.txt.gz 2019-11-19 11:59 66 gc5BaseBw.sql 2019-11-19 11:59 1.3K gbLoaded.txt.gz 2020-08-22 01:02 38K gbLoaded.sql 2020-08-22 01:02 1.6K gap.txt.gz 2019-11-19 10:40 28 gap.sql 2019-11-19 10:40 1.6K cytoBandIdeo.txt.gz 2019-11-19 12:34 91K cytoBandIdeo.sql 2019-11-19 12:34 1.5K cpgIslandExtUnmasked.txt.gz 2019-11-19 13:32 1.1M cpgIslandExtUnmasked.sql 2019-11-19 13:32 1.7K cpgIslandExt.txt.gz 2019-11-20 11:07 615K cpgIslandExt.sql 2019-11-20 11:07 1.7K chromInfo.txt.gz 2019-11-19 12:34 93K chromInfo.sql 2019-11-19 12:34 1.4K chainPanTro5Link.txt.gz 2016-10-21 12:55 244M chainPanTro5Link.sql 2016-10-21 12:55 1.5K chainPanTro5.txt.gz 2016-10-21 12:54 80M chainPanTro5.sql 2016-10-21 12:54 1.7K chainPanTro4Link.txt.gz 2016-10-21 12:54 167M chainPanTro4Link.sql 2016-10-21 12:53 1.5K chainPanTro4.txt.gz 2016-10-21 12:53 41M chainPanTro4.sql 2016-10-21 12:53 1.7K chainPanPan2Link.txt.gz 2017-12-24 07:09 109M chainPanPan2Link.sql 2017-12-24 07:09 1.5K chainPanPan2.txt.gz 2017-12-24 07:09 10M chainPanPan2.sql 2017-12-24 07:09 1.7K chainHg38Link.txt.gz 2019-11-21 10:07 239M chainHg38Link.sql 2019-11-21 10:07 1.6K chainHg38.txt.gz 2019-11-21 10:06 68M chainHg38.sql 2019-11-21 10:06 1.7K bigFiles.txt.gz 2024-03-24 03:33 69 bigFiles.sql 2024-03-24 03:33 1.4K augustusGene.txt.gz 2019-11-20 14:04 2.2M augustusGene.sql 2019-11-20 14:04 2.0K all_mrna.txt.gz 2019-12-05 11:48 24K all_mrna.sql 2019-12-05 11:48 2.1K