This directory contains a dump of the UCSC genome annotation database for the
    Aug. 2015 (MPI-EVA panpan1.1/panPan2) assembly of the bonobo genome
    (panPan2, Max-Planck Institute for Evolutionary Anthropology) .

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/10729
    http://www.ncbi.nlm.nih.gov/genome/assembly/474211
    http://www.ncbi.nlm.nih.gov/bioproject/169343

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=panPan2
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/panPan2/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/panPan2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/panPan2/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/panPan2/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/panPan2/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 panPan2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql panPan2 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

-----------------------------------------------------------------------------
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 - all_mrna.sql 2020-08-22 17:09 2.1K all_mrna.txt.gz 2020-08-22 17:09 14K augustusGene.sql 2017-12-20 11:12 1.9K augustusGene.txt.gz 2017-12-20 11:12 2.2M bigFiles.sql 2021-05-02 03:04 1.4K bigFiles.txt.gz 2021-05-02 03:04 95 chainGorGor5.sql 2017-12-20 11:12 1.7K chainGorGor5.txt.gz 2017-12-20 11:12 11M chainGorGor5Link.sql 2017-12-20 11:12 1.5K chainGorGor5Link.txt.gz 2017-12-20 11:12 110M chainHg38.sql 2017-12-20 11:13 1.7K chainHg38.txt.gz 2017-12-20 11:13 37M chainHg38Link.sql 2017-12-20 11:13 1.5K chainHg38Link.txt.gz 2017-12-20 11:13 130M chainMm10.sql 2017-12-20 11:14 1.7K chainMm10.txt.gz 2017-12-20 11:14 56M chainMm10Link.sql 2017-12-20 11:14 1.5K chainMm10Link.txt.gz 2017-12-20 11:15 484M chainPanTro4.sql 2017-12-20 11:17 1.7K chainPanTro4.txt.gz 2017-12-20 11:17 19M chainPanTro4Link.sql 2017-12-20 11:17 1.5K chainPanTro4Link.txt.gz 2017-12-20 11:17 77M chromAlias.sql 2017-12-20 11:17 1.4K chromAlias.txt.gz 2017-12-20 11:17 105K chromInfo.sql 2017-12-20 11:17 1.4K chromInfo.txt.gz 2017-12-20 11:17 48K cpgIslandExt.sql 2017-12-20 11:17 1.7K cpgIslandExt.txt.gz 2017-12-20 11:17 589K cpgIslandExtUnmasked.sql 2017-12-20 11:17 1.7K cpgIslandExtUnmasked.txt.gz 2017-12-20 11:17 920K cytoBandIdeo.sql 2017-12-20 11:18 1.5K cytoBandIdeo.txt.gz 2017-12-20 11:18 54K ensGene.sql 2020-08-31 15:48 1.9K ensGene.txt.gz 2020-08-31 15:48 3.1M ensGtp.sql 2020-08-31 15:48 1.4K ensGtp.txt.gz 2020-08-31 15:48 475K ensPep.sql 2020-08-31 16:23 1.3K ensPep.txt.gz 2020-08-31 16:23 7.0M ensemblSource.sql 2020-08-31 16:23 1.4K ensemblSource.txt.gz 2020-08-31 16:23 149K ensemblToGeneName.sql 2020-08-31 15:48 1.4K ensemblToGeneName.txt.gz 2020-08-31 15:48 229K extNcbiRefSeq.sql 2020-05-10 03:28 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:28 91 gap.sql 2017-12-20 11:18 1.6K gap.txt.gz 2017-12-20 11:18 1.4M gapOverlap.sql 2017-12-20 11:18 1.8K gapOverlap.txt.gz 2017-12-20 11:18 2.3K gbLoaded.sql 2020-08-22 17:50 1.6K gbLoaded.txt.gz 2020-08-22 17:50 13K gc5BaseBw.sql 2017-12-20 11:12 1.3K gc5BaseBw.txt.gz 2017-12-20 11:12 66 genscan.sql 2017-12-20 11:12 1.7K genscan.txt.gz 2017-12-20 11:12 2.5M genscanSubopt.sql 2017-12-20 11:13 1.6K genscanSubopt.txt.gz 2017-12-20 11:13 5.1M gold.sql 2017-12-20 11:14 1.7K gold.txt.gz 2017-12-20 11:14 2.1M grp.sql 2017-12-20 11:17 1.3K grp.txt.gz 2017-12-20 11:17 213 hgFindSpec.sql 2020-10-25 08:17 1.7K hgFindSpec.txt.gz 2020-10-25 08:17 1.2K history.sql 2017-12-20 11:17 1.6K history.txt.gz 2017-12-20 11:17 1.0K microsat.sql 2017-12-20 11:17 1.5K microsat.txt.gz 2017-12-20 11:17 298K mrnaOrientInfo.sql 2020-08-22 17:09 1.8K mrnaOrientInfo.txt.gz 2020-08-22 17:09 8.5K ncbiRefSeq.sql 2020-05-10 03:28 1.9K ncbiRefSeq.txt.gz 2020-05-10 03:28 3.2M ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K ncbiRefSeqCds.txt.gz 2020-05-10 03:28 351K ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 6.1K ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.6M ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75 ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 10M ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 3.2M ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 4.2M nestedRepeats.sql 2017-12-20 11:18 1.9K nestedRepeats.txt.gz 2017-12-20 11:18 17M netGorGor5.sql 2017-12-20 11:12 2.1K netGorGor5.txt.gz 2017-12-20 11:12 7.0M netHg38.sql 2017-12-20 11:13 2.1K netHg38.txt.gz 2017-12-20 11:13 6.2M netMm10.sql 2017-12-20 11:14 2.1K netMm10.txt.gz 2017-12-20 11:14 71M netPanTro4.sql 2017-12-20 11:17 2.1K netPanTro4.txt.gz 2017-12-20 11:17 6.4M refFlat.sql 2020-08-22 17:28 1.7K refFlat.txt.gz 2020-08-22 17:28 7.1K refGene.sql 2020-08-22 17:25 1.9K refGene.txt.gz 2020-08-22 17:25 8.1K refSeqAli.sql 2019-07-28 06:01 2.1K refSeqAli.txt.gz 2019-07-28 06:01 8.2K rmsk.sql 2017-12-20 11:18 1.9K rmsk.txt.gz 2017-12-20 11:18 134M seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:28 903K simpleRepeat.sql 2017-12-20 11:18 1.9K simpleRepeat.txt.gz 2017-12-20 11:18 21M tableDescriptions.sql 2021-01-14 06:34 1.4K tableDescriptions.txt.gz 2021-01-14 06:34 6.4K tableList.sql 2021-05-02 03:04 1.6K tableList.txt.gz 2021-05-02 03:04 3.5K tandemDups.sql 2017-12-20 11:18 1.8K tandemDups.txt.gz 2017-12-20 11:18 16M trackDb.sql 2020-10-25 01:05 2.0K trackDb.txt.gz 2020-10-25 01:05 39K ucscToINSDC.sql 2017-12-20 11:18 1.4K ucscToINSDC.txt.gz 2017-12-20 11:18 79K ucscToRefSeq.sql 2017-12-20 11:18 1.4K ucscToRefSeq.txt.gz 2017-12-20 11:18 79K windowmaskerSdust.sql 2017-12-20 11:18 1.5K windowmaskerSdust.txt.gz 2017-12-20 11:19 142M xenoRefFlat.sql 2020-08-22 17:50 1.7K xenoRefFlat.txt.gz 2020-08-22 17:50 23M xenoRefGene.sql 2020-08-22 17:50 1.9K xenoRefGene.txt.gz 2020-08-22 17:50 26M xenoRefSeqAli.sql 2020-08-22 17:50 2.1K xenoRefSeqAli.txt.gz 2020-08-22 17:50 24M