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