This directory contains a dump of the UCSC genome annotation database for
the Feb. 2011 (CSAC 2.1.4/panTro4) assembly of the chimp genome (panTro4, CSAC Pan_troglodytes-2.1.4 (GCA_000001515.4))
from the Chimp 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/202
    http://www.ncbi.nlm.nih.gov/genome/assembly/255628
    http://www.ncbi.nlm.nih.gov/bioproject/13184

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=panTro4
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/panTro4/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/panTro4/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/panTro4/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro4/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro4/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 panTro4 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql panTro4 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

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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.
-----------------------------------------------------------------------------
      Name                        Last modified      Size  Description
Parent Directory - all_est.sql 2016-07-10 09:12 2.1K all_est.txt.gz 2016-07-10 09:12 875K all_mrna.sql 2020-05-08 18:29 2.1K all_mrna.txt.gz 2020-05-08 18:29 303K augustusGene.sql 2015-07-26 17:21 1.9K augustusGene.txt.gz 2015-07-26 17:21 2.2M bigFiles.sql 2022-12-04 03:11 1.4K bigFiles.txt.gz 2022-12-04 03:11 94 chainGorGor5.sql 2016-10-30 09:32 1.7K chainGorGor5.txt.gz 2016-10-30 09:32 44M chainGorGor5Link.sql 2016-10-30 09:32 1.5K chainGorGor5Link.txt.gz 2016-10-30 09:33 174M chainHg19.sql 2013-06-24 23:02 1.7K chainHg19.txt.gz 2013-06-24 23:02 28M chainHg19Link.sql 2013-06-24 23:02 1.5K chainHg19Link.txt.gz 2013-06-24 23:02 125M chainMm10.sql 2012-11-21 16:14 1.7K chainMm10.txt.gz 2012-11-21 16:14 67M chainMm10Link.sql 2012-11-21 16:08 1.5K chainMm10Link.txt.gz 2012-11-21 16:08 523M chainPanPan2.sql 2017-12-24 08:43 1.7K chainPanPan2.txt.gz 2017-12-24 08:43 19M chainPanPan2Link.sql 2017-12-24 08:43 1.5K chainPanPan2Link.txt.gz 2017-12-24 08:43 80M chainRheMac3.sql 2012-11-21 16:10 1.7K chainRheMac3.txt.gz 2012-11-21 16:10 15M chainRheMac3Link.sql 2012-11-21 16:17 1.6K chainRheMac3Link.txt.gz 2012-11-21 16:18 168M chainRn5.sql 2014-01-26 17:25 1.7K chainRn5.txt.gz 2014-01-26 17:25 54M chainRn5Link.sql 2014-01-26 17:25 1.5K chainRn5Link.txt.gz 2014-01-26 17:26 492M chainTarSyr2.sql 2015-05-25 08:02 1.7K chainTarSyr2.txt.gz 2015-05-25 08:02 304M chainTarSyr2Link.sql 2015-05-25 08:03 1.5K chainTarSyr2Link.txt.gz 2015-05-25 08:05 1.2G chromAlias.sql 2018-02-18 08:11 1.4K chromAlias.txt.gz 2018-02-18 08:11 266K chromInfo.sql 2012-11-21 16:08 1.4K chromInfo.txt.gz 2012-11-21 16:08 139K cpgIslandExt.sql 2012-11-21 16:07 1.7K cpgIslandExt.txt.gz 2012-11-21 16:07 627K cpgIslandExtUnmasked.sql 2014-06-01 18:33 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 18:33 1.0M cytoBandIdeo.sql 2013-04-28 20:31 1.5K cytoBandIdeo.txt.gz 2013-04-28 20:31 133K ensGene.sql 2018-02-04 08:51 1.9K ensGene.txt.gz 2018-02-04 08:51 2.3M ensGtp.sql 2018-02-04 08:51 1.4K ensGtp.txt.gz 2018-02-04 08:51 282K ensPep.sql 2018-02-04 08:51 1.3K ensPep.txt.gz 2018-02-04 08:51 5.9M ensemblSource.sql 2018-02-04 08:51 1.4K ensemblSource.txt.gz 2018-02-04 08:51 96K ensemblToGeneName.sql 2018-02-04 08:52 1.4K ensemblToGeneName.txt.gz 2018-02-04 08:52 140K estOrientInfo.sql 2016-07-10 09:13 1.8K estOrientInfo.txt.gz 2016-07-10 09:13 221K extNcbiRefSeq.sql 2018-08-14 02:23 1.5K extNcbiRefSeq.txt.gz 2018-08-14 02:23 89 gap.sql 2012-11-21 16:08 1.6K gap.txt.gz 2012-11-21 16:08 2.3M gbLoaded.sql 2020-08-22 18:36 1.6K gbLoaded.txt.gz 2020-08-22 18:36 41K gc5BaseBw.sql 2012-11-21 16:21 1.3K gc5BaseBw.txt.gz 2012-11-21 16:21 63 geneid.sql 2015-11-22 20:24 1.9K geneid.txt.gz 2015-11-22 20:24 2.6M genscan.sql 2012-11-21 16:14 1.7K genscan.txt.gz 2012-11-21 16:14 2.9M gold.sql 2012-11-21 16:08 1.7K gold.txt.gz 2012-11-21 16:08 607K grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.sql 2021-12-27 12:20 1.8K hgFindSpec.txt.gz 2021-12-27 12:20 1.2K history.sql 2012-11-21 16:14 1.6K history.txt.gz 2012-11-21 16:14 647 intronEst.sql 2016-07-10 09:13 2.1K intronEst.txt.gz 2016-07-10 09:13 677K microsat.sql 2015-08-23 23:56 1.5K microsat.txt.gz 2015-08-23 23:56 350K mrnaOrientInfo.sql 2020-08-22 18:33 1.8K mrnaOrientInfo.txt.gz 2020-08-22 18:33 110K ncbiRefSeq.sql 2018-02-09 13:49 2.0K ncbiRefSeq.txt.gz 2018-02-09 13:49 3.5M ncbiRefSeqCds.sql 2018-08-14 02:23 1.4K ncbiRefSeqCds.txt.gz 2018-08-14 02:23 391K ncbiRefSeqCurated.sql 2018-02-09 13:49 2.0K ncbiRefSeqCurated.txt.gz 2018-02-09 13:49 192K ncbiRefSeqLink.sql 2018-02-09 13:49 2.0K ncbiRefSeqLink.txt.gz 2018-02-09 13:49 1.9M ncbiRefSeqOther.sql 2018-08-14 02:23 1.3K ncbiRefSeqOther.txt.gz 2018-08-14 02:23 75 ncbiRefSeqPepTable.sql 2018-08-14 02:23 1.4K ncbiRefSeqPepTable.txt.gz 2018-08-14 02:23 10M ncbiRefSeqPredicted.sql 2018-02-09 13:49 2.0K ncbiRefSeqPredicted.txt.gz 2018-02-09 13:49 3.4M ncbiRefSeqPsl.sql 2018-02-09 13:49 2.1K ncbiRefSeqPsl.txt.gz 2018-02-09 13:49 4.7M nestedRepeats.sql 2012-11-21 16:14 1.9K nestedRepeats.txt.gz 2012-11-21 16:14 18M netGorGor5.sql 2016-10-30 09:33 2.1K netGorGor5.txt.gz 2016-10-30 09:33 11M netHg19.sql 2013-06-24 23:02 2.1K netHg19.txt.gz 2013-06-24 23:02 10M netMm10.sql 2012-11-21 16:20 2.1K netMm10.txt.gz 2012-11-21 16:20 73M netPanPan2.sql 2017-12-24 08:43 2.1K netPanPan2.txt.gz 2017-12-24 08:43 11M netRheMac3.sql 2012-11-21 16:14 2.1K netRheMac3.txt.gz 2012-11-21 16:14 29M netRn5.sql 2014-01-26 17:28 2.1K netRn5.txt.gz 2014-01-26 17:28 72M netTarSyr2.sql 2015-05-25 08:09 2.1K netTarSyr2.txt.gz 2015-05-25 08:09 69M refFlat.sql 2020-08-22 18:27 1.7K refFlat.txt.gz 2020-08-22 18:27 201K refGene.sql 2020-08-22 18:27 1.9K refGene.txt.gz 2020-08-22 18:27 219K refSeqAli.sql 2020-08-22 18:33 2.1K refSeqAli.txt.gz 2020-08-22 18:33 225K rmsk.sql 2012-11-21 16:14 1.9K rmsk.txt.gz 2012-11-21 16:15 139M seqNcbiRefSeq.sql 2018-08-14 02:23 1.6K seqNcbiRefSeq.txt.gz 2018-08-14 02:23 1.0M simpleRepeat.sql 2012-11-21 16:07 1.9K simpleRepeat.txt.gz 2012-11-21 16:07 26M tableDescriptions.sql 2021-08-07 06:33 1.4K tableDescriptions.txt.gz 2021-08-07 06:33 6.7K tableList.sql 2022-12-04 03:11 1.6K tableList.txt.gz 2022-12-04 03:11 4.2K trackDb.sql 2021-12-27 12:20 2.1K trackDb.txt.gz 2021-12-27 12:20 36K ucscToEnsembl.sql 2012-11-21 16:16 1.4K ucscToEnsembl.txt.gz 2012-11-21 16:16 156K ucscToINSDC.sql 2013-09-15 18:11 1.4K ucscToINSDC.txt.gz 2013-09-15 18:11 192K ucscToRefSeq.sql 2018-02-18 08:11 1.4K ucscToRefSeq.txt.gz 2018-02-18 08:11 198K windowmaskerSdust.sql 2012-11-21 16:13 1.5K windowmaskerSdust.txt.gz 2012-11-21 16:13 151M xenoMrna.sql 2020-08-22 18:06 2.1K xenoMrna.txt.gz 2020-08-22 18:06 321M xenoRefFlat.sql 2020-08-22 18:32 1.7K xenoRefFlat.txt.gz 2020-08-22 18:32 30M xenoRefGene.sql 2020-08-22 18:27 1.9K xenoRefGene.txt.gz 2020-08-22 18:27 33M xenoRefSeqAli.sql 2020-08-22 18:33 2.1K xenoRefSeqAli.txt.gz 2020-08-22 18:33 31M