This directory contains a dump of the UCSC genome annotation database for
the Mar. 2012 (Baylor Panu_2.0/papAnu2) assembly of the baboon genome (papAnu2, Baylor College of Medicine).
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/394
    http://www.ncbi.nlm.nih.gov/genome/assembly/383538
    http://www.ncbi.nlm.nih.gov/bioproject/54005

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=papAnu2
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/papAnu2/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/papAnu2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/papAnu2/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/papAnu2/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/papAnu2/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 papAnu2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql papAnu2 --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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.

      Name                        Last modified      Size  Description
Parent Directory - xenoRefSeqAli.txt.gz 2020-08-22 22:18 35M xenoRefSeqAli.sql 2020-08-22 22:18 2.1K xenoRefGene.txt.gz 2020-08-22 22:18 36M xenoRefGene.sql 2020-08-22 22:18 1.9K xenoRefFlat.txt.gz 2020-08-22 22:18 33M xenoRefFlat.sql 2020-08-22 22:18 1.7K xenoMrna.txt.gz 2020-08-22 21:58 344M xenoMrna.sql 2020-08-22 21:58 2.1K windowmaskerSdust.txt.gz 2013-01-22 13:00 144M windowmaskerSdust.sql 2013-01-22 13:00 1.5K ucscToRefSeq.txt.gz 2018-02-18 08:15 454K ucscToRefSeq.sql 2018-02-18 08:15 1.4K ucscToEnsembl.txt.gz 2015-04-13 05:01 299K ucscToEnsembl.sql 2015-04-13 05:01 1.4K trackDb.txt.gz 2021-01-21 09:36 37K trackDb.sql 2021-01-21 09:36 2.1K tableList.txt.gz 2021-06-13 03:16 2.7K tableList.sql 2021-06-13 03:16 1.6K tableDescriptions.txt.gz 2019-07-21 03:43 5.3K tableDescriptions.sql 2019-07-21 03:43 1.4K simpleRepeat.txt.gz 2013-01-22 12:58 29M simpleRepeat.sql 2013-01-22 12:58 1.9K rmsk.txt.gz 2013-01-22 12:58 137M rmsk.sql 2013-01-22 12:58 1.9K refSeqAli.txt.gz 2020-05-08 21:41 47K refSeqAli.sql 2020-05-08 21:41 2.1K refGene.txt.gz 2020-08-22 22:18 45K refGene.sql 2020-08-22 22:18 1.9K refFlat.txt.gz 2020-08-22 22:18 41K refFlat.sql 2020-08-22 22:18 1.7K netTarSyr2.txt.gz 2015-05-25 08:21 71M netTarSyr2.sql 2015-05-25 08:21 2.1K nestedRepeats.txt.gz 2013-01-22 12:58 18M nestedRepeats.sql 2013-01-22 12:58 1.9K mrnaOrientInfo.txt.gz 2020-05-08 21:41 17K mrnaOrientInfo.sql 2020-05-08 21:41 1.8K microsat.txt.gz 2015-08-24 00:04 314K microsat.sql 2015-08-24 00:04 1.5K intronEst.txt.gz 2016-07-10 09:15 3.1M intronEst.sql 2016-07-10 09:15 2.1K history.txt.gz 2013-01-22 13:01 375 history.sql 2013-01-22 13:01 1.6K hgFindSpec.txt.gz 2021-01-21 09:36 779 hgFindSpec.sql 2021-01-21 09:36 1.8K grp.txt.gz 2014-03-02 04:14 208 grp.sql 2014-03-02 04:14 1.3K gold.txt.gz 2013-01-22 13:02 1.0M gold.sql 2013-01-22 13:02 1.7K genscanSubopt.txt.gz 2013-01-22 13:01 5.9M genscanSubopt.sql 2013-01-22 13:01 1.6K genscan.txt.gz 2013-01-22 13:01 2.5M genscan.sql 2013-01-22 13:01 1.7K geneid.txt.gz 2015-11-22 20:32 2.1M geneid.sql 2015-11-22 20:32 1.9K gc5BaseBw.txt.gz 2013-01-22 13:01 63 gc5BaseBw.sql 2013-01-22 13:01 1.3K gbLoaded.txt.gz 2020-08-22 22:18 41K gbLoaded.sql 2020-08-22 22:18 1.6K gap.txt.gz 2013-01-22 13:04 1.7M gap.sql 2013-01-22 13:04 1.6K estOrientInfo.txt.gz 2016-07-10 09:15 1.7M estOrientInfo.sql 2016-07-10 09:15 1.8K ensemblToGeneName.txt.gz 2018-02-04 08:57 156K ensemblToGeneName.sql 2018-02-04 08:57 1.4K ensemblSource.txt.gz 2018-02-04 08:56 93K ensemblSource.sql 2018-02-04 08:56 1.4K ensPep.txt.gz 2018-02-04 08:54 6.4M ensPep.sql 2018-02-04 08:54 1.3K ensGtp.txt.gz 2018-02-04 08:54 302K ensGtp.sql 2018-02-04 08:54 1.4K ensGene.txt.gz 2018-02-04 08:56 2.3M ensGene.sql 2018-02-04 08:56 1.9K cytoBandIdeo.txt.gz 2013-04-28 20:39 308K cytoBandIdeo.sql 2013-04-28 20:39 1.5K cpgIslandExtUnmasked.txt.gz 2014-06-01 18:39 1.7M cpgIslandExtUnmasked.sql 2014-06-01 18:39 1.7K cpgIslandExt.txt.gz 2013-01-22 12:58 597K cpgIslandExt.sql 2013-01-22 12:58 1.7K chromInfo.txt.gz 2013-01-22 13:02 300K chromInfo.sql 2013-01-22 13:02 1.4K chromAlias.txt.gz 2018-02-18 08:15 615K chromAlias.sql 2018-02-18 08:15 1.4K chainTarSyr2Link.txt.gz 2015-05-25 08:18 832M chainTarSyr2Link.sql 2015-05-25 08:16 1.5K chainTarSyr2.txt.gz 2015-05-25 08:21 129M chainTarSyr2.sql 2015-05-25 08:21 1.7K bigFiles.txt.gz 2021-06-13 03:16 68 bigFiles.sql 2021-06-13 03:16 1.4K augustusGene.txt.gz 2015-07-26 17:21 1.9M augustusGene.sql 2015-07-26 17:21 1.9K all_mrna.txt.gz 2020-03-01 08:34 38K all_mrna.sql 2020-03-01 08:34 2.1K all_est.txt.gz 2016-07-10 09:15 6.2M all_est.sql 2016-07-10 09:15 2.1K