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.

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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/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;'

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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 - gc5BaseBw.txt.gz 2017-12-20 11:12 66 ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75 extNcbiRefSeq.txt.gz 2020-05-10 03:28 91 bigFiles.txt.gz 2024-10-06 03:10 95 grp.txt.gz 2017-12-20 11:17 213 history.txt.gz 2017-12-20 11:17 1.0K hgFindSpec.txt.gz 2023-12-05 13:50 1.2K gc5BaseBw.sql 2017-12-20 11:12 1.3K ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K ensPep.sql 2021-05-25 14:43 1.3K grp.sql 2017-12-20 11:17 1.3K ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K ensemblSource.sql 2021-05-25 14:43 1.4K chromInfo.sql 2017-12-20 11:17 1.4K bigFiles.sql 2024-10-06 03:10 1.4K ensemblToGeneName.sql 2021-05-25 14:42 1.4K chromAlias.sql 2017-12-20 11:17 1.4K ucscToINSDC.sql 2017-12-20 11:18 1.4K ucscToRefSeq.sql 2017-12-20 11:18 1.4K extNcbiRefSeq.sql 2020-05-10 03:28 1.4K ensGtp.sql 2021-05-25 14:42 1.4K tableDescriptions.sql 2024-10-05 02:03 1.5K microsat.sql 2017-12-20 11:17 1.5K windowmaskerSdust.sql 2017-12-20 11:18 1.5K cytoBandIdeo.sql 2017-12-20 11:18 1.5K chainHg38Link.sql 2017-12-20 11:13 1.5K chainMm10Link.sql 2017-12-20 11:14 1.5K seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K chainGorGor5Link.sql 2017-12-20 11:12 1.5K chainPanTro4Link.sql 2017-12-20 11:17 1.5K genscanSubopt.sql 2017-12-20 11:13 1.6K history.sql 2017-12-20 11:17 1.6K tableList.sql 2024-10-06 03:10 1.6K gap.sql 2017-12-20 11:18 1.6K gbLoaded.sql 2020-08-22 17:50 1.6K gold.sql 2017-12-20 11:14 1.7K genscan.sql 2017-12-20 11:12 1.7K cpgIslandExt.sql 2017-12-20 11:17 1.7K chainHg38.sql 2017-12-20 11:13 1.7K chainMm10.sql 2017-12-20 11:14 1.7K chainGorGor5.sql 2017-12-20 11:12 1.7K chainPanTro4.sql 2017-12-20 11:17 1.7K cpgIslandExtUnmasked.sql 2017-12-20 11:17 1.7K refFlat.sql 2020-08-22 17:28 1.7K xenoRefFlat.sql 2020-08-22 17:50 1.7K hgFindSpec.sql 2023-12-05 13:50 1.8K gapOverlap.sql 2017-12-20 11:18 1.8K tandemDups.sql 2017-12-20 11:18 1.8K mrnaOrientInfo.sql 2020-08-22 17:09 1.8K rmsk.sql 2017-12-20 11:18 1.9K simpleRepeat.sql 2017-12-20 11:18 1.9K ncbiRefSeq.sql 2020-05-10 03:28 1.9K nestedRepeats.sql 2017-12-20 11:18 1.9K augustusGene.sql 2017-12-20 11:12 1.9K ensGene.sql 2021-05-25 14:42 1.9K refGene.sql 2020-08-22 17:25 1.9K ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K xenoRefGene.sql 2020-08-22 17:50 2.0K ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K trackDb.sql 2023-12-05 13:50 2.1K netHg38.sql 2017-12-20 11:13 2.1K netMm10.sql 2017-12-20 11:14 2.1K netGorGor5.sql 2017-12-20 11:12 2.1K netPanTro4.sql 2017-12-20 11:17 2.1K refSeqAli.sql 2019-07-28 06:01 2.1K ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K all_mrna.sql 2020-08-22 17:09 2.1K xenoRefSeqAli.sql 2020-08-22 17:50 2.1K gapOverlap.txt.gz 2017-12-20 11:18 2.3K tableList.txt.gz 2024-10-06 03:10 3.5K ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 6.1K tableDescriptions.txt.gz 2024-10-05 02:03 6.7K refFlat.txt.gz 2020-08-22 17:28 7.1K refGene.txt.gz 2020-08-22 17:25 8.1K refSeqAli.txt.gz 2019-07-28 06:01 8.2K mrnaOrientInfo.txt.gz 2020-08-22 17:09 8.5K gbLoaded.txt.gz 2020-08-22 17:50 13K all_mrna.txt.gz 2020-08-22 17:09 14K trackDb.txt.gz 2023-12-05 13:50 32K chromInfo.txt.gz 2017-12-20 11:17 48K cytoBandIdeo.txt.gz 2017-12-20 11:18 54K ucscToINSDC.txt.gz 2017-12-20 11:18 79K ucscToRefSeq.txt.gz 2017-12-20 11:18 79K chromAlias.txt.gz 2017-12-20 11:17 105K ensemblSource.txt.gz 2021-05-25 14:43 149K ensemblToGeneName.txt.gz 2021-05-25 14:42 199K microsat.txt.gz 2017-12-20 11:17 298K ncbiRefSeqCds.txt.gz 2020-05-10 03:28 351K ensGtp.txt.gz 2021-05-25 14:42 437K cpgIslandExt.txt.gz 2017-12-20 11:17 589K seqNcbiRefSeq.txt.gz 2020-05-10 03:28 903K cpgIslandExtUnmasked.txt.gz 2017-12-20 11:17 920K gap.txt.gz 2017-12-20 11:18 1.4M ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.6M gold.txt.gz 2017-12-20 11:14 2.1M augustusGene.txt.gz 2017-12-20 11:12 2.2M genscan.txt.gz 2017-12-20 11:12 2.5M ensGene.txt.gz 2021-05-25 14:42 3.1M ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 3.2M ncbiRefSeq.txt.gz 2020-05-10 03:28 3.2M ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 4.2M genscanSubopt.txt.gz 2017-12-20 11:13 5.1M netHg38.txt.gz 2017-12-20 11:13 6.2M netPanTro4.txt.gz 2017-12-20 11:17 6.4M netGorGor5.txt.gz 2017-12-20 11:12 7.0M ensPep.txt.gz 2021-05-25 14:43 7.0M ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 10M chainGorGor5.txt.gz 2017-12-20 11:12 11M tandemDups.txt.gz 2017-12-20 11:18 16M nestedRepeats.txt.gz 2017-12-20 11:18 17M chainPanTro4.txt.gz 2017-12-20 11:17 19M simpleRepeat.txt.gz 2017-12-20 11:18 21M xenoRefFlat.txt.gz 2020-08-22 17:50 23M xenoRefSeqAli.txt.gz 2020-08-22 17:50 24M xenoRefGene.txt.gz 2020-08-22 17:50 26M chainHg38.txt.gz 2017-12-20 11:13 37M chainMm10.txt.gz 2017-12-20 11:14 56M netMm10.txt.gz 2017-12-20 11:14 71M chainPanTro4Link.txt.gz 2017-12-20 11:17 77M chainGorGor5Link.txt.gz 2017-12-20 11:12 110M chainHg38Link.txt.gz 2017-12-20 11:13 130M rmsk.txt.gz 2017-12-20 11:18 134M windowmaskerSdust.txt.gz 2017-12-20 11:19 142M chainMm10Link.txt.gz 2017-12-20 11:15 484M