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