This directory contains a dump of the UCSC genome annotation database for
the Jun. 2011 (GGSC Nleu1.1/nomLeu2) assembly of the gibbon genome (nomLeu2, Gibbon Genome Sequencing Consortium Nleu1.1 (NCBI project 13975, GCA_000146795.2, WGS ADFV01)).
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/480
    http://www.ncbi.nlm.nih.gov/genome/assembly/313108
    http://www.ncbi.nlm.nih.gov/bioproject/13975

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=nomLeu2
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/nomLeu2/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/nomLeu2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/nomLeu2/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu2/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu2/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 nomLeu2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql nomLeu2 --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.

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All the files and tables in this directory are freely usable for any purpose.
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      Name                        Last modified      Size  Description
Parent Directory - augustusGene.sql 2015-07-26 16:56 1.9K augustusGene.txt.gz 2015-07-26 16:56 2.1M bigFiles.sql 2021-10-17 03:10 1.4K bigFiles.txt.gz 2021-10-17 03:10 68 chainMm10.sql 2012-11-16 11:58 1.7K chainMm10.txt.gz 2012-11-16 11:58 57M chainMm10Link.sql 2012-11-16 11:59 1.5K chainMm10Link.txt.gz 2012-11-16 12:00 463M chromInfo.sql 2012-11-16 12:03 1.4K chromInfo.txt.gz 2012-11-16 12:03 90K cpgIslandExt.sql 2012-11-16 11:56 1.7K cpgIslandExt.txt.gz 2012-11-16 11:56 581K cpgIslandExtUnmasked.sql 2014-06-01 17:23 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 17:23 1.3M cytoBandIdeo.sql 2013-04-28 19:26 1.5K cytoBandIdeo.txt.gz 2013-04-28 19:26 88K gap.sql 2012-11-16 12:03 1.6K gap.txt.gz 2012-11-16 12:03 2.3M gbLoaded.sql 2020-08-22 12:49 1.6K gbLoaded.txt.gz 2020-08-22 12:49 23K gc5BaseBw.sql 2012-11-16 11:56 1.3K gc5BaseBw.txt.gz 2012-11-16 11:56 63 genscan.sql 2012-11-16 11:58 1.7K genscan.txt.gz 2012-11-16 11:58 2.7M gold.sql 2012-11-16 11:58 1.7K gold.txt.gz 2012-11-16 11:58 3.2M grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.sql 2021-08-02 14:31 1.8K hgFindSpec.txt.gz 2021-08-02 14:31 443 history.sql 2012-11-16 11:58 1.6K history.txt.gz 2012-11-16 11:58 513 microsat.sql 2015-08-23 22:22 1.5K microsat.txt.gz 2015-08-23 22:22 320K nestedRepeats.sql 2012-11-16 11:55 1.9K nestedRepeats.txt.gz 2012-11-16 11:55 17M netMm10.sql 2012-11-16 11:58 2.1K netMm10.txt.gz 2012-11-16 11:58 70M rmsk.sql 2012-11-16 11:58 1.9K rmsk.txt.gz 2012-11-16 11:59 130M simpleRepeat.sql 2012-11-16 11:58 1.9K simpleRepeat.txt.gz 2012-11-16 11:58 22M tableDescriptions.sql 2019-07-21 03:43 1.4K tableDescriptions.txt.gz 2019-07-21 03:43 4.7K tableList.sql 2021-10-17 03:10 1.6K tableList.txt.gz 2021-10-17 03:10 1.9K trackDb.sql 2021-08-02 14:31 2.1K trackDb.txt.gz 2021-08-02 14:31 17K windowmaskerSdust.sql 2012-11-16 12:02 1.5K windowmaskerSdust.txt.gz 2012-11-16 12:03 139M xenoMrna.sql 2016-02-21 20:41 2.1K xenoMrna.txt.gz 2016-02-21 20:42 314M xenoRefFlat.sql 2020-08-22 12:49 1.7K xenoRefFlat.txt.gz 2020-08-22 12:49 38M xenoRefGene.sql 2020-08-22 12:49 1.9K xenoRefGene.txt.gz 2020-08-22 12:49 42M xenoRefSeqAli.sql 2020-08-22 12:49 2.1K xenoRefSeqAli.txt.gz 2020-08-22 12:49 44M