This directory contains a dump of the UCSC genome annotation database for
the Nov. 2008 (Baylor Pham_1.0/papHam1) assembly of the baboon genome (papHam1, Baylor BCM HGSC Pham_1.0).
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/778
    http://www.ncbi.nlm.nih.gov/genome/assembly/N/A
    http://www.ncbi.nlm.nih.gov/bioproject/20425

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=papHam1
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/papHam1/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/papHam1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/papHam1/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/papHam1/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/papHam1/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 papHam1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql papHam1 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

For conditions of use regarding the Baboon genome sequence data, see
http://www.hgsc.bcm.edu/content/conditions-use

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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 - all_mrna.sql 2020-03-01 08:35 2.1K all_mrna.txt.gz 2020-03-01 08:35 33K augustusGene.sql 2015-07-26 17:21 1.9K augustusGene.txt.gz 2015-07-26 17:21 2.0M bigFiles.sql 2022-06-19 03:04 1.4K bigFiles.txt.gz 2022-06-19 03:04 33 chainCalJac3.sql 2012-11-16 12:07 1.7K chainCalJac3.txt.gz 2012-11-16 12:07 16M chainCalJac3Link.sql 2012-11-16 12:16 1.6K chainCalJac3Link.txt.gz 2012-11-16 12:16 213M chainGorGor3.sql 2012-11-16 12:14 1.7K chainGorGor3.txt.gz 2012-11-16 12:14 19M chainGorGor3Link.sql 2012-11-16 12:14 1.6K chainGorGor3Link.txt.gz 2012-11-16 12:15 150M chainMacFas5.sql 2016-04-10 03:33 1.7K chainMacFas5.txt.gz 2016-04-10 03:33 24M chainMacFas5Link.sql 2016-04-10 03:33 1.5K chainMacFas5Link.txt.gz 2016-04-10 03:33 84M chainMm10.sql 2012-11-16 12:15 1.7K chainMm10.txt.gz 2012-11-16 12:15 59M chainMm10Link.sql 2012-11-16 12:07 1.5K chainMm10Link.txt.gz 2012-11-16 12:08 444M chromInfo.sql 2012-11-16 12:04 1.4K chromInfo.txt.gz 2012-11-16 12:04 1.6M cpgIslandExt.sql 2012-11-16 12:07 1.7K cpgIslandExt.txt.gz 2012-11-16 12:07 597K cpgIslandExtUnmasked.sql 2014-06-01 18:46 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 18:46 1.3M cytoBandIdeo.sql 2013-04-28 20:45 1.5K cytoBandIdeo.txt.gz 2013-04-28 20:45 1.8M gap.sql 2012-11-16 12:04 1.7K gap.txt.gz 2012-11-16 12:04 3.8M gbLoaded.sql 2020-08-20 03:50 1.6K gbLoaded.txt.gz 2020-08-20 03:50 15K gc5Base.sql 2012-11-16 12:17 1.9K gc5Base.txt.gz 2012-11-16 12:17 19M genscan.sql 2012-11-16 12:18 1.7K genscan.txt.gz 2012-11-16 12:18 2.8M gold.sql 2012-11-16 12:11 1.8K gold.txt.gz 2012-11-16 12:11 9.5M grp.sql 2014-03-02 04:14 1.4K grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.sql 2021-08-02 14:32 1.8K hgFindSpec.txt.gz 2021-08-02 14:32 563 history.sql 2012-11-16 12:18 1.6K history.txt.gz 2012-11-16 12:18 768 microsat.sql 2015-08-24 00:13 1.5K microsat.txt.gz 2015-08-24 00:13 303K mrnaOrientInfo.sql 2020-05-07 00:58 1.8K mrnaOrientInfo.txt.gz 2020-05-07 00:58 19K nestedRepeats.sql 2012-11-16 12:17 2.1K nestedRepeats.txt.gz 2012-11-16 12:17 16M netCalJac3.sql 2012-11-16 12:13 2.1K netCalJac3.txt.gz 2012-11-16 12:13 49M netGorGor3.sql 2012-11-16 12:15 2.1K netGorGor3.txt.gz 2012-11-16 12:15 33M netMacFas5.sql 2016-04-10 03:34 2.1K netMacFas5.txt.gz 2016-04-10 03:34 21M netMm10.sql 2012-11-16 12:13 2.1K netMm10.txt.gz 2012-11-16 12:13 70M quality.sql 2012-11-16 12:11 1.9K quality.txt.gz 2012-11-16 12:11 68M refFlat.sql 2020-08-20 03:30 1.7K refFlat.txt.gz 2020-08-20 03:30 40K refGene.sql 2020-08-20 03:30 1.9K refGene.txt.gz 2020-08-20 03:30 46K refSeqAli.sql 2020-05-07 00:58 2.1K refSeqAli.txt.gz 2020-05-07 00:58 51K rmsk.sql 2012-11-16 12:13 2.1K rmsk.txt.gz 2012-11-16 12:13 135M simpleRepeat.sql 2012-11-16 12:07 2.1K simpleRepeat.txt.gz 2012-11-16 12:07 25M tableDescriptions.sql 2019-07-21 03:43 1.4K tableDescriptions.txt.gz 2019-07-21 03:43 5.3K tableList.sql 2022-06-19 03:04 1.6K tableList.txt.gz 2022-06-19 03:04 2.8K trackDb.sql 2021-08-02 14:32 2.1K trackDb.txt.gz 2021-08-02 14:32 28K windowmaskerSdust.sql 2012-11-16 12:16 1.5K windowmaskerSdust.txt.gz 2012-11-16 12:16 151M xenoMrna.sql 2016-02-21 22:26 2.1K xenoMrna.txt.gz 2016-02-21 22:27 317M xenoRefFlat.sql 2020-08-20 03:50 1.7K xenoRefFlat.txt.gz 2020-08-20 03:50 32M xenoRefGene.sql 2020-08-20 03:50 1.9K xenoRefGene.txt.gz 2020-08-20 03:50 35M xenoRefSeqAli.sql 2020-08-20 03:50 2.1K xenoRefSeqAli.txt.gz 2020-08-20 03:50 39M