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.

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