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 - gc5BaseBw.txt.gz 2013-05-23 11:51 63 ncbiRefSeqOther.txt.gz 2022-05-26 12:22 75 extNcbiRefSeq.txt.gz 2022-05-26 12:22 91 bigFiles.txt.gz 2022-10-02 03:11 94 grp.txt.gz 2014-03-02 04:14 208 history.txt.gz 2013-05-23 11:47 390 hgFindSpec_pushedout.txt.gz 2021-12-27 12:19 758 hgFindSpec.txt.gz 2022-05-27 17:26 1.1K gc5BaseBw.sql 2013-05-23 11:51 1.3K ncbiRefSeqOther.sql 2022-05-26 12:22 1.3K ensPep.sql 2021-05-25 14:41 1.3K grp.sql 2014-03-02 04:14 1.3K ncbiRefSeqCds.sql 2022-05-26 12:22 1.4K bigFiles.sql 2022-10-02 03:11 1.4K ensemblSource.sql 2021-05-25 14:41 1.4K ncbiRefSeqPepTable.sql 2022-05-26 12:22 1.4K chromInfo.sql 2013-05-23 11:45 1.4K ensemblToGeneName.sql 2021-05-25 14:40 1.4K chromAlias.sql 2018-02-04 08:28 1.4K tableDescriptions.sql 2022-05-28 06:34 1.4K ucscToINSDC.sql 2013-09-15 17:09 1.4K ucscToRefSeq.sql 2018-02-04 08:28 1.4K ensGtp.sql 2021-05-25 14:40 1.4K extNcbiRefSeq.sql 2022-05-26 12:22 1.5K microsat.sql 2015-08-23 22:29 1.5K windowmaskerSdust.sql 2013-05-23 11:52 1.5K chainHg38Link.sql 2018-01-07 09:30 1.5K chainHg19Link.sql 2013-05-23 11:50 1.5K cytoBandIdeo.sql 2022-05-26 12:48 1.5K chainTarSyr2Link.sql 2015-05-25 06:26 1.5K tableList.sql 2022-10-02 03:11 1.6K genscanSubopt.sql 2013-05-23 11:48 1.6K seqNcbiRefSeq.sql 2022-05-26 12:22 1.6K history.sql 2013-05-23 11:47 1.6K gbLoaded.sql 2020-08-19 21:42 1.6K gap.sql 2013-05-23 11:50 1.6K gold.sql 2013-05-23 11:53 1.7K genscan.sql 2013-05-23 11:47 1.7K cpgIslandExt.sql 2013-05-23 11:50 1.7K chainHg38.sql 2018-01-07 09:29 1.7K chainHg19.sql 2013-05-23 11:52 1.7K chainTarSyr2.sql 2015-05-25 06:32 1.7K cpgIslandExtUnmasked.sql 2014-06-01 17:28 1.7K xenoRefFlat.sql 2020-08-19 21:38 1.7K hgFindSpec.sql 2022-05-27 17:26 1.8K hgFindSpec_pushedout.sql 2021-12-27 12:19 1.8K rmsk.sql 2013-05-23 11:46 1.9K geneid.sql 2015-11-22 19:41 1.9K simpleRepeat.sql 2013-05-23 11:50 1.9K nestedRepeats.sql 2013-05-23 11:45 1.9K xenoRefGene.sql 2020-08-19 21:38 1.9K augustusGene.sql 2015-07-26 17:03 1.9K ensGene.sql 2021-05-25 14:40 1.9K ncbiRefSeq.sql 2022-05-26 12:18 2.0K ncbiRefSeqCurated.sql 2022-05-26 12:18 2.0K ncbiRefSeqPredicted.sql 2022-05-26 12:18 2.0K ncbiRefSeqLink.sql 2022-05-26 12:19 2.0K trackDb.sql 2022-05-27 17:26 2.1K trackDb_pushedout.sql 2021-12-27 12:19 2.1K netHg38.sql 2018-01-07 09:34 2.1K netHg19.sql 2013-05-23 11:45 2.1K netTarSyr2.sql 2015-05-25 06:31 2.1K xenoMrna.sql 2020-08-19 21:23 2.1K xenoRefSeqAli.sql 2020-08-19 21:42 2.1K ncbiRefSeqPsl.sql 2022-05-26 12:19 2.1K ncbiRefSeqCurated.txt.gz 2022-05-26 12:18 2.5K tableList.txt.gz 2022-10-02 03:11 3.2K tableDescriptions.txt.gz 2022-05-28 06:34 6.2K gbLoaded.txt.gz 2020-08-19 21:42 29K trackDb_pushedout.txt.gz 2021-12-27 12:19 37K trackDb.txt.gz 2022-05-27 17:26 42K chromInfo.txt.gz 2013-05-23 11:45 92K cytoBandIdeo.txt.gz 2022-05-26 12:48 93K ensemblSource.txt.gz 2021-05-25 14:41 138K ucscToINSDC.txt.gz 2013-09-15 17:09 139K ucscToRefSeq.txt.gz 2018-02-04 08:28 142K chromAlias.txt.gz 2018-02-04 08:28 202K ensemblToGeneName.txt.gz 2021-05-25 14:40 222K ncbiRefSeqCds.txt.gz 2022-05-26 12:22 264K microsat.txt.gz 2015-08-23 22:29 329K ensGtp.txt.gz 2021-05-25 14:40 476K cpgIslandExt.txt.gz 2013-05-23 11:50 594K seqNcbiRefSeq.txt.gz 2022-05-26 12:22 668K cpgIslandExtUnmasked.txt.gz 2014-06-01 17:28 1.3M ncbiRefSeqLink.txt.gz 2022-05-26 12:19 1.3M augustusGene.txt.gz 2015-07-26 17:03 2.1M geneid.txt.gz 2015-11-22 19:41 2.1M gap.txt.gz 2013-05-23 11:50 2.4M genscan.txt.gz 2013-05-23 11:47 2.7M ncbiRefSeqPredicted.txt.gz 2022-05-26 12:18 2.8M ncbiRefSeq.txt.gz 2022-05-26 12:18 2.8M ensGene.txt.gz 2021-05-25 14:40 2.9M ncbiRefSeqPsl.txt.gz 2022-05-26 12:19 3.3M gold.txt.gz 2013-05-23 11:53 3.3M genscanSubopt.txt.gz 2013-05-23 11:48 5.6M ncbiRefSeqPepTable.txt.gz 2022-05-26 12:22 8.2M ensPep.txt.gz 2021-05-25 14:41 12M netHg19.txt.gz 2013-05-23 11:45 16M chainHg19.txt.gz 2013-05-23 11:52 16M nestedRepeats.txt.gz 2013-05-23 11:45 16M netHg38.txt.gz 2018-01-07 09:34 16M simpleRepeat.txt.gz 2013-05-23 11:50 23M xenoRefFlat.txt.gz 2020-08-19 21:38 23M xenoRefGene.txt.gz 2020-08-19 21:38 26M xenoRefSeqAli.txt.gz 2020-08-19 21:42 26M netTarSyr2.txt.gz 2015-05-25 06:31 66M rmsk.txt.gz 2013-05-23 11:47 129M chainHg19Link.txt.gz 2013-05-23 11:50 138M windowmaskerSdust.txt.gz 2013-05-23 11:52 140M xenoMrna.txt.gz 2020-08-19 21:23 245M chainHg38.txt.gz 2018-01-07 09:29 246M chainTarSyr2.txt.gz 2015-05-25 06:32 278M chainHg38Link.txt.gz 2018-01-07 09:31 753M chainTarSyr2Link.txt.gz 2015-05-25 06:27 1.1G