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 - netHg19.sql 2013-05-23 11:45 2.1K netHg19.txt.gz 2013-05-23 11:45 16M nestedRepeats.sql 2013-05-23 11:45 1.9K nestedRepeats.txt.gz 2013-05-23 11:45 16M chromInfo.sql 2013-05-23 11:45 1.4K chromInfo.txt.gz 2013-05-23 11:45 92K rmsk.sql 2013-05-23 11:46 1.9K rmsk.txt.gz 2013-05-23 11:47 129M genscan.sql 2013-05-23 11:47 1.7K genscan.txt.gz 2013-05-23 11:47 2.7M history.sql 2013-05-23 11:47 1.6K history.txt.gz 2013-05-23 11:47 390 genscanSubopt.sql 2013-05-23 11:48 1.6K genscanSubopt.txt.gz 2013-05-23 11:48 5.6M cpgIslandExt.sql 2013-05-23 11:50 1.7K cpgIslandExt.txt.gz 2013-05-23 11:50 594K simpleRepeat.sql 2013-05-23 11:50 1.9K simpleRepeat.txt.gz 2013-05-23 11:50 23M gap.sql 2013-05-23 11:50 1.6K chainHg19Link.sql 2013-05-23 11:50 1.5K gap.txt.gz 2013-05-23 11:50 2.4M chainHg19Link.txt.gz 2013-05-23 11:50 138M gc5BaseBw.sql 2013-05-23 11:51 1.3K gc5BaseBw.txt.gz 2013-05-23 11:51 63 chainHg19.sql 2013-05-23 11:52 1.7K chainHg19.txt.gz 2013-05-23 11:52 16M windowmaskerSdust.sql 2013-05-23 11:52 1.5K windowmaskerSdust.txt.gz 2013-05-23 11:52 140M gold.sql 2013-05-23 11:53 1.7K gold.txt.gz 2013-05-23 11:53 3.3M ucscToINSDC.sql 2013-09-15 17:09 1.4K ucscToINSDC.txt.gz 2013-09-15 17:09 139K grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 cpgIslandExtUnmasked.sql 2014-06-01 17:28 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 17:28 1.3M chainTarSyr2Link.sql 2015-05-25 06:26 1.5K chainTarSyr2Link.txt.gz 2015-05-25 06:27 1.1G netTarSyr2.sql 2015-05-25 06:31 2.1K netTarSyr2.txt.gz 2015-05-25 06:31 66M chainTarSyr2.sql 2015-05-25 06:32 1.7K chainTarSyr2.txt.gz 2015-05-25 06:32 278M augustusGene.sql 2015-07-26 17:03 1.9K augustusGene.txt.gz 2015-07-26 17:03 2.1M microsat.sql 2015-08-23 22:29 1.5K microsat.txt.gz 2015-08-23 22:29 329K geneid.sql 2015-11-22 19:41 1.9K geneid.txt.gz 2015-11-22 19:41 2.1M 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 netHg38.sql 2018-01-07 09:34 2.1K netHg38.txt.gz 2018-01-07 09:34 16M chromAlias.sql 2018-02-04 08:28 1.4K chromAlias.txt.gz 2018-02-04 08:28 202K ucscToRefSeq.sql 2018-02-04 08:28 1.4K ucscToRefSeq.txt.gz 2018-02-04 08:28 142K xenoMrna.sql 2020-08-19 21:23 2.1K xenoMrna.txt.gz 2020-08-19 21:23 245M xenoRefGene.sql 2020-08-19 21:38 1.9K xenoRefGene.txt.gz 2020-08-19 21:38 26M xenoRefFlat.sql 2020-08-19 21:38 1.7K xenoRefFlat.txt.gz 2020-08-19 21:38 23M xenoRefSeqAli.sql 2020-08-19 21:42 2.1K xenoRefSeqAli.txt.gz 2020-08-19 21:42 26M gbLoaded.sql 2020-08-19 21:42 1.6K gbLoaded.txt.gz 2020-08-19 21:42 29K ensGene.sql 2021-05-25 14:40 1.9K ensGene.txt.gz 2021-05-25 14:40 2.9M ensGtp.sql 2021-05-25 14:40 1.4K ensGtp.txt.gz 2021-05-25 14:40 476K ensemblToGeneName.sql 2021-05-25 14:40 1.4K ensemblToGeneName.txt.gz 2021-05-25 14:40 222K ensemblSource.sql 2021-05-25 14:41 1.4K ensemblSource.txt.gz 2021-05-25 14:41 138K ensPep.sql 2021-05-25 14:41 1.3K ensPep.txt.gz 2021-05-25 14:41 12M trackDb_pushedout.sql 2021-12-27 12:19 2.1K trackDb_pushedout.txt.gz 2021-12-27 12:19 37K hgFindSpec_pushedout.sql 2021-12-27 12:19 1.8K hgFindSpec_pushedout.txt.gz 2021-12-27 12:19 758 ncbiRefSeq.sql 2022-05-26 12:18 2.0K ncbiRefSeq.txt.gz 2022-05-26 12:18 2.8M ncbiRefSeqCurated.sql 2022-05-26 12:18 2.0K ncbiRefSeqCurated.txt.gz 2022-05-26 12:18 2.5K ncbiRefSeqPredicted.sql 2022-05-26 12:18 2.0K ncbiRefSeqPredicted.txt.gz 2022-05-26 12:18 2.8M ncbiRefSeqLink.sql 2022-05-26 12:19 2.0K ncbiRefSeqLink.txt.gz 2022-05-26 12:19 1.3M ncbiRefSeqPsl.sql 2022-05-26 12:19 2.1K ncbiRefSeqPsl.txt.gz 2022-05-26 12:19 3.3M ncbiRefSeqPepTable.sql 2022-05-26 12:22 1.4K ncbiRefSeqPepTable.txt.gz 2022-05-26 12:22 8.2M ncbiRefSeqOther.sql 2022-05-26 12:22 1.3K ncbiRefSeqOther.txt.gz 2022-05-26 12:22 75 extNcbiRefSeq.sql 2022-05-26 12:22 1.5K extNcbiRefSeq.txt.gz 2022-05-26 12:22 91 ncbiRefSeqCds.sql 2022-05-26 12:22 1.4K ncbiRefSeqCds.txt.gz 2022-05-26 12:22 264K seqNcbiRefSeq.sql 2022-05-26 12:22 1.6K seqNcbiRefSeq.txt.gz 2022-05-26 12:22 668K cytoBandIdeo.sql 2022-05-26 12:48 1.5K cytoBandIdeo.txt.gz 2022-05-26 12:48 93K trackDb.sql 2022-05-27 17:26 2.1K trackDb.txt.gz 2022-05-27 17:26 42K hgFindSpec.sql 2022-05-27 17:26 1.8K hgFindSpec.txt.gz 2022-05-27 17:26 1.1K tableDescriptions.sql 2022-05-28 06:34 1.4K tableDescriptions.txt.gz 2022-05-28 06:34 6.2K tableList.sql 2022-08-07 03:10 1.6K tableList.txt.gz 2022-08-07 03:10 3.2K bigFiles.sql 2022-08-07 03:10 1.4K bigFiles.txt.gz 2022-08-07 03:10 94