This directory contains a dump of the UCSC genome annotation database for
the Jan. 2010 (GGSC Nleu1.0/nomLeu1) assembly of the gibbon genome (nomLeu1, GGSC (NCBI project 13975, accession GCA_000146795.1)).
The annotations were generated by UCSC and collaborators worldwide.

This assembly was produced by the National Center for Biotechnology Information (NCBI).
For more information on the gibbon genome, see the project website:
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=nomLeu1
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/nomLeu1/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/nomLeu1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/nomLeu1/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu1/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu1/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 nomLeu1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql nomLeu1 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

All the files and tables in this directory are freely usable for any purpose.

      Name                     Last modified      Size  Description
Parent Directory - all_mrna.sql 2020-08-22 12:49 2.1K all_mrna.txt.gz 2020-08-22 12:49 8.4K augustusGene.sql 2015-07-26 16:56 1.9K augustusGene.txt.gz 2015-07-26 16:56 2.1M bigFiles.sql 2021-05-16 03:09 1.4K bigFiles.txt.gz 2021-05-16 03:09 68 chainGorGor3.sql 2011-11-22 15:50 1.6K chainGorGor3.txt.gz 2011-11-22 15:50 15M chainGorGor3Link.sql 2011-11-22 15:47 1.5K chainGorGor3Link.txt.gz 2011-11-22 15:47 121M chainHg19.sql 2011-11-22 15:50 1.6K chainHg19.txt.gz 2011-11-22 15:50 16M chainHg19Link.sql 2011-11-22 15:54 1.5K chainHg19Link.txt.gz 2011-11-22 15:55 136M chainMm10.sql 2012-10-21 03:41 1.7K chainMm10.txt.gz 2012-10-21 03:41 57M chainMm10Link.sql 2012-10-21 03:39 1.5K chainMm10Link.txt.gz 2012-10-21 03:39 464M chromAlias.sql 2016-09-15 18:00 1.4K chromAlias.txt.gz 2016-09-15 18:00 91K chromInfo.sql 2011-11-22 15:52 1.3K chromInfo.txt.gz 2011-11-22 15:52 90K ensGene.sql 2018-02-04 08:25 1.9K ensGene.txt.gz 2018-02-04 08:25 2.2M ensGtp.sql 2018-02-04 08:25 1.4K ensGtp.txt.gz 2018-02-04 08:25 280K ensPep.sql 2018-02-04 08:24 1.3K ensPep.txt.gz 2018-02-04 08:24 6.0M ensemblSource.sql 2018-02-04 08:24 1.4K ensemblSource.txt.gz 2018-02-04 08:24 85K ensemblToGeneName.sql 2018-02-04 08:25 1.4K ensemblToGeneName.txt.gz 2018-02-04 08:25 154K gap.sql 2011-11-22 15:54 1.5K gap.txt.gz 2011-11-22 15:54 2.3M gbLoaded.sql 2020-08-22 13:34 1.6K gbLoaded.txt.gz 2020-08-22 13:34 15K gc5BaseBw.sql 2011-11-22 15:50 1.2K gc5BaseBw.txt.gz 2011-11-22 15:50 63 gold.sql 2011-11-22 15:47 1.6K gold.txt.gz 2011-11-22 15:47 3.2M grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.sql 2020-10-25 08:13 1.7K hgFindSpec.txt.gz 2020-10-25 08:13 667 history.sql 2011-11-22 15:53 1.5K history.txt.gz 2011-11-22 15:53 433 microsat.sql 2015-08-23 22:14 1.5K microsat.txt.gz 2015-08-23 22:14 320K mrnaOrientInfo.sql 2020-08-22 12:49 1.8K mrnaOrientInfo.txt.gz 2020-08-22 12:49 3.2K nestedRepeats.sql 2011-11-22 15:47 1.9K nestedRepeats.txt.gz 2011-11-22 15:47 16M netGorGor3.sql 2011-11-22 15:54 2.0K netGorGor3.txt.gz 2011-11-22 15:54 20M netHg19.sql 2011-11-22 15:52 2.0K netHg19.txt.gz 2011-11-22 15:52 16M netMm10.sql 2012-10-21 03:38 2.1K netMm10.txt.gz 2012-10-21 03:39 70M rmsk.sql 2011-11-22 15:53 1.8K rmsk.txt.gz 2011-11-22 15:53 128M simpleRepeat.sql 2011-11-22 15:51 1.9K simpleRepeat.txt.gz 2011-11-22 15:51 22M tRNAs.sql 2012-04-16 03:21 1.7K tRNAs.txt.gz 2012-04-16 03:21 10K tableDescriptions.sql 2020-10-10 02:03 1.4K tableDescriptions.txt.gz 2020-10-10 02:03 5.2K tableList.sql 2021-05-16 03:09 1.6K tableList.txt.gz 2021-05-16 03:09 2.3K trackDb.sql 2020-10-25 08:13 2.0K trackDb.txt.gz 2020-10-25 08:13 18K xenoMrna.sql 2016-02-21 20:37 2.1K xenoMrna.txt.gz 2016-02-21 20:37 301M xenoRefFlat.sql 2020-08-22 13:34 1.7K xenoRefFlat.txt.gz 2020-08-22 13:34 30M xenoRefGene.sql 2020-08-22 13:34 1.9K xenoRefGene.txt.gz 2020-08-22 13:34 33M xenoRefSeqAli.sql 2020-08-22 13:34 2.1K xenoRefSeqAli.txt.gz 2020-08-22 13:34 32M