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 - netGorGor5.sql 2017-12-20 11:12 2.1K netGorGor5.txt.gz 2017-12-20 11:12 7.0M augustusGene.sql 2017-12-20 11:12 1.9K augustusGene.txt.gz 2017-12-20 11:12 2.2M chainGorGor5.sql 2017-12-20 11:12 1.7K chainGorGor5.txt.gz 2017-12-20 11:12 11M gc5BaseBw.sql 2017-12-20 11:12 1.3K gc5BaseBw.txt.gz 2017-12-20 11:12 66 chainGorGor5Link.sql 2017-12-20 11:12 1.5K genscan.sql 2017-12-20 11:12 1.7K genscan.txt.gz 2017-12-20 11:12 2.5M chainGorGor5Link.txt.gz 2017-12-20 11:12 110M netHg38.sql 2017-12-20 11:13 2.1K netHg38.txt.gz 2017-12-20 11:13 6.2M chainHg38.sql 2017-12-20 11:13 1.7K chainHg38.txt.gz 2017-12-20 11:13 37M genscanSubopt.sql 2017-12-20 11:13 1.6K genscanSubopt.txt.gz 2017-12-20 11:13 5.1M chainHg38Link.sql 2017-12-20 11:13 1.5K chainHg38Link.txt.gz 2017-12-20 11:13 130M netMm10.sql 2017-12-20 11:14 2.1K netMm10.txt.gz 2017-12-20 11:14 71M 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 gold.sql 2017-12-20 11:14 1.7K gold.txt.gz 2017-12-20 11:14 2.1M chainMm10Link.txt.gz 2017-12-20 11:15 484M chainPanTro4.sql 2017-12-20 11:17 1.7K grp.sql 2017-12-20 11:17 1.3K grp.txt.gz 2017-12-20 11:17 213 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 history.sql 2017-12-20 11:17 1.6K history.txt.gz 2017-12-20 11:17 1.0K netPanTro4.sql 2017-12-20 11:17 2.1K netPanTro4.txt.gz 2017-12-20 11:17 6.4M 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 microsat.sql 2017-12-20 11:17 1.5K microsat.txt.gz 2017-12-20 11:17 298K cytoBandIdeo.sql 2017-12-20 11:18 1.5K cytoBandIdeo.txt.gz 2017-12-20 11:18 54K gap.sql 2017-12-20 11:18 1.6K gap.txt.gz 2017-12-20 11:18 1.4M rmsk.sql 2017-12-20 11:18 1.9K rmsk.txt.gz 2017-12-20 11:18 134M nestedRepeats.sql 2017-12-20 11:18 1.9K nestedRepeats.txt.gz 2017-12-20 11:18 17M gapOverlap.sql 2017-12-20 11:18 1.8K gapOverlap.txt.gz 2017-12-20 11:18 2.3K simpleRepeat.sql 2017-12-20 11:18 1.9K simpleRepeat.txt.gz 2017-12-20 11:18 21M tandemDups.sql 2017-12-20 11:18 1.8K tandemDups.txt.gz 2017-12-20 11:18 16M 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 refSeqAli.sql 2019-07-28 06:01 2.1K refSeqAli.txt.gz 2019-07-28 06:01 8.2K extNcbiRefSeq.sql 2020-05-10 03:28 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:28 91 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 seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:28 903K all_mrna.sql 2020-08-22 17:09 2.1K all_mrna.txt.gz 2020-08-22 17:09 14K mrnaOrientInfo.sql 2020-08-22 17:09 1.8K mrnaOrientInfo.txt.gz 2020-08-22 17:09 8.5K refGene.sql 2020-08-22 17:25 1.9K refGene.txt.gz 2020-08-22 17:25 8.1K refFlat.sql 2020-08-22 17:28 1.7K refFlat.txt.gz 2020-08-22 17:28 7.1K xenoRefGene.sql 2020-08-22 17:50 2.0K xenoRefGene.txt.gz 2020-08-22 17:50 26M xenoRefFlat.sql 2020-08-22 17:50 1.7K xenoRefFlat.txt.gz 2020-08-22 17:50 23M xenoRefSeqAli.sql 2020-08-22 17:50 2.1K xenoRefSeqAli.txt.gz 2020-08-22 17:50 24M gbLoaded.sql 2020-08-22 17:50 1.6K gbLoaded.txt.gz 2020-08-22 17:50 13K ensGene.sql 2021-05-25 14:42 1.9K ensGene.txt.gz 2021-05-25 14:42 3.1M ensGtp.sql 2021-05-25 14:42 1.4K ensGtp.txt.gz 2021-05-25 14:42 437K ensemblToGeneName.sql 2021-05-25 14:42 1.4K ensemblToGeneName.txt.gz 2021-05-25 14:42 199K ensemblSource.sql 2021-05-25 14:43 1.4K ensemblSource.txt.gz 2021-05-25 14:43 149K ensPep.sql 2021-05-25 14:43 1.3K ensPep.txt.gz 2021-05-25 14:43 7.0M trackDb.sql 2023-12-05 13:50 2.1K trackDb.txt.gz 2023-12-05 13:50 32K trackDb_pushedout.sql 2023-12-05 13:50 2.1K trackDb_pushedout.txt.gz 2023-12-05 13:50 32K hgFindSpec.sql 2023-12-05 13:50 1.8K hgFindSpec.txt.gz 2023-12-05 13:50 1.2K hgFindSpec_pushedout.sql 2023-12-05 13:50 1.8K hgFindSpec_pushedout.txt.gz 2023-12-05 13:50 1.2K tableDescriptions.sql 2024-03-23 02:03 1.4K tableDescriptions.txt.gz 2024-03-23 02:03 6.7K tableList.sql 2024-03-24 03:08 1.6K tableList.txt.gz 2024-03-24 03:08 3.7K bigFiles.sql 2024-03-24 03:08 1.4K bigFiles.txt.gz 2024-03-24 03:08 95