This directory contains a dump of the UCSC genome annotation database for the
    Oct. 2012 (Nleu_3.0/nomLeu3) assembly of the gibbon genome
    (nomLeu3, Gibbon Genome Sequencing Consortium ) .

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/506498
    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=nomLeu3
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/nomLeu3/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/nomLeu3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/nomLeu3/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu3/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu3/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 nomLeu3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql nomLeu3 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

-----------------------------------------------------------------------------
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 - augustusGene.sql 2015-07-26 17:03 1.9K augustusGene.txt.gz 2015-07-26 17:03 2.1M bigFiles.sql 2021-05-02 03:12 1.4K bigFiles.txt.gz 2021-05-02 03:12 68 chainHg19.sql 2013-05-23 11:52 1.7K chainHg19.txt.gz 2013-05-23 11:52 16M chainHg19Link.sql 2013-05-23 11:50 1.5K chainHg19Link.txt.gz 2013-05-23 11:50 138M chainHg38.sql 2018-01-07 09:29 1.7K chainHg38.txt.gz 2018-01-07 09:29 246M chainHg38Link.sql 2018-01-07 09:30 1.5K chainHg38Link.txt.gz 2018-01-07 09:31 753M chainTarSyr2.sql 2015-05-25 06:32 1.7K chainTarSyr2.txt.gz 2015-05-25 06:32 278M chainTarSyr2Link.sql 2015-05-25 06:26 1.5K chainTarSyr2Link.txt.gz 2015-05-25 06:27 1.1G chromAlias.sql 2018-02-04 08:28 1.4K chromAlias.txt.gz 2018-02-04 08:28 202K chromInfo.sql 2013-05-23 11:45 1.4K chromInfo.txt.gz 2013-05-23 11:45 92K cpgIslandExt.sql 2013-05-23 11:50 1.7K cpgIslandExt.txt.gz 2013-05-23 11:50 594K cpgIslandExtUnmasked.sql 2014-06-01 17:28 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 17:28 1.3M ensGene.sql 2020-08-31 15:45 1.9K ensGene.txt.gz 2020-08-31 15:45 2.9M ensGtp.sql 2020-08-31 15:45 1.4K ensGtp.txt.gz 2020-08-31 15:45 467K ensPep.sql 2020-08-31 16:22 1.3K ensPep.txt.gz 2020-08-31 16:22 12M ensemblSource.sql 2020-08-31 16:22 1.4K ensemblSource.txt.gz 2020-08-31 16:22 138K ensemblToGeneName.sql 2020-08-31 15:45 1.4K ensemblToGeneName.txt.gz 2020-08-31 15:45 230K gap.sql 2013-05-23 11:50 1.6K gap.txt.gz 2013-05-23 11:50 2.4M gbLoaded.sql 2020-08-19 21:42 1.6K gbLoaded.txt.gz 2020-08-19 21:42 29K gc5BaseBw.sql 2013-05-23 11:51 1.3K gc5BaseBw.txt.gz 2013-05-23 11:51 63 geneid.sql 2015-11-22 19:41 1.9K geneid.txt.gz 2015-11-22 19:41 2.1M genscan.sql 2013-05-23 11:47 1.7K genscan.txt.gz 2013-05-23 11:47 2.7M genscanSubopt.sql 2013-05-23 11:48 1.6K genscanSubopt.txt.gz 2013-05-23 11:48 5.6M gold.sql 2013-05-23 11:53 1.7K gold.txt.gz 2013-05-23 11:53 3.3M grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.sql 2020-12-06 08:13 1.7K hgFindSpec.txt.gz 2020-12-06 08:13 748 history.sql 2013-05-23 11:47 1.6K history.txt.gz 2013-05-23 11:47 390 microsat.sql 2015-08-23 22:29 1.5K microsat.txt.gz 2015-08-23 22:29 329K nestedRepeats.sql 2013-05-23 11:45 1.9K nestedRepeats.txt.gz 2013-05-23 11:45 16M netHg19.sql 2013-05-23 11:45 2.1K netHg19.txt.gz 2013-05-23 11:45 16M netHg38.sql 2018-01-07 09:34 2.1K netHg38.txt.gz 2018-01-07 09:34 16M netTarSyr2.sql 2015-05-25 06:31 2.1K netTarSyr2.txt.gz 2015-05-25 06:31 66M rmsk.sql 2013-05-23 11:46 1.9K rmsk.txt.gz 2013-05-23 11:47 129M simpleRepeat.sql 2013-05-23 11:50 1.9K simpleRepeat.txt.gz 2013-05-23 11:50 23M tableDescriptions.sql 2019-07-21 03:43 1.4K tableDescriptions.txt.gz 2019-07-21 03:43 5.1K tableList.sql 2021-05-02 03:12 1.6K tableList.txt.gz 2021-05-02 03:12 2.4K trackDb.sql 2020-12-02 14:09 2.0K trackDb.txt.gz 2020-12-02 14:09 35K ucscToINSDC.sql 2013-09-15 17:09 1.4K ucscToINSDC.txt.gz 2013-09-15 17:09 139K ucscToRefSeq.sql 2018-02-04 08:28 1.4K ucscToRefSeq.txt.gz 2018-02-04 08:28 142K windowmaskerSdust.sql 2013-05-23 11:52 1.5K windowmaskerSdust.txt.gz 2013-05-23 11:52 140M xenoMrna.sql 2020-08-19 21:23 2.1K xenoMrna.txt.gz 2020-08-19 21:23 245M xenoRefFlat.sql 2020-08-19 21:38 1.7K xenoRefFlat.txt.gz 2020-08-19 21:38 23M xenoRefGene.sql 2020-08-19 21:38 1.9K xenoRefGene.txt.gz 2020-08-19 21:38 26M xenoRefSeqAli.sql 2020-08-19 21:42 2.1K xenoRefSeqAli.txt.gz 2020-08-19 21:42 26M