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