This directory contains a dump of the UCSC genome annotation database for the
    May 2020 (Mhudiblu_PPA_v0/panPan3) assembly of the bonobo genome
    (panPan3, University of Washington) .

The annotations were generated by UCSC and collaborators worldwide.

For more information about this assembly, please note the NCBI resources:

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:
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, then go to
the directory goldenPath/panPan3/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:// .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync:// .

Or with wget, all files:
    wget --timestamping 
With wget, a single file:
    wget --timestamping 
        -O gc5Base.txt.gz

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 panPan3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql panPan3 --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 - gap.sql 12-Jun-2020 10:45 1.6K gap.txt.gz 12-Jun-2020 10:45 11K gold.sql 12-Jun-2020 10:45 1.7K gold.txt.gz 12-Jun-2020 10:45 66K cpgIslandExtUnmasked.sql 12-Jun-2020 11:36 1.7K cpgIslandExtUnmasked.txt.gz 12-Jun-2020 11:36 1.0M chromAlias.sql 12-Jun-2020 12:33 1.4K chromAlias.txt.gz 12-Jun-2020 12:33 93K simpleRepeat.sql 12-Jun-2020 17:08 1.9K simpleRepeat.txt.gz 12-Jun-2020 17:08 26M cytoBandIdeo.sql 12-Jun-2020 17:27 1.5K cytoBandIdeo.txt.gz 12-Jun-2020 17:27 27K gc5BaseBw.sql 12-Jun-2020 17:27 1.3K gc5BaseBw.txt.gz 12-Jun-2020 17:27 66 grp.sql 12-Jun-2020 17:27 1.3K grp.txt.gz 12-Jun-2020 17:27 213 ucscToINSDC.sql 12-Jun-2020 17:27 1.4K ucscToINSDC.txt.gz 12-Jun-2020 17:27 39K ucscToRefSeq.sql 12-Jun-2020 17:27 1.4K ucscToRefSeq.txt.gz 12-Jun-2020 17:27 37K chromInfo.sql 12-Jun-2020 18:00 1.4K chromInfo.txt.gz 12-Jun-2020 18:00 27K rmsk.sql 12-Jun-2020 18:21 1.9K rmsk.txt.gz 12-Jun-2020 18:21 139M nestedRepeats.sql 12-Jun-2020 18:23 1.9K nestedRepeats.txt.gz 12-Jun-2020 18:23 18M windowmaskerSdust.sql 12-Jun-2020 19:56 1.5K windowmaskerSdust.txt.gz 12-Jun-2020 19:56 145M microsat.sql 13-Jun-2020 10:04 1.5K microsat.txt.gz 13-Jun-2020 10:04 304K ncbiRefSeq.sql 13-Jun-2020 10:16 1.9K ncbiRefSeq.txt.gz 13-Jun-2020 10:16 4.0M ncbiRefSeqCurated.sql 13-Jun-2020 10:16 2.0K ncbiRefSeqCurated.txt.gz 13-Jun-2020 10:16 8.5K ncbiRefSeqPredicted.sql 13-Jun-2020 10:16 2.0K ncbiRefSeqPredicted.txt.gz 13-Jun-2020 10:16 4.0M ncbiRefSeqLink.sql 13-Jun-2020 10:16 2.0K ncbiRefSeqLink.txt.gz 13-Jun-2020 10:16 2.2M ncbiRefSeqPsl.sql 13-Jun-2020 10:16 2.1K ncbiRefSeqPsl.txt.gz 13-Jun-2020 10:16 5.7M ncbiRefSeqOther.sql 13-Jun-2020 15:32 1.3K ncbiRefSeqOther.txt.gz 13-Jun-2020 15:32 75 ncbiRefSeqPepTable.sql 13-Jun-2020 15:32 1.4K ncbiRefSeqPepTable.txt.gz 13-Jun-2020 15:32 12M extNcbiRefSeq.sql 13-Jun-2020 15:42 1.4K extNcbiRefSeq.txt.gz 13-Jun-2020 15:42 91 ncbiRefSeqCds.sql 13-Jun-2020 15:42 1.3K ncbiRefSeqCds.txt.gz 13-Jun-2020 15:42 500K seqNcbiRefSeq.sql 13-Jun-2020 15:42 1.5K seqNcbiRefSeq.txt.gz 13-Jun-2020 15:42 1.3M cpgIslandExt.sql 15-Jun-2020 09:12 1.7K cpgIslandExt.txt.gz 15-Jun-2020 09:12 625K augustusGene.sql 15-Jun-2020 12:26 1.9K augustusGene.txt.gz 15-Jun-2020 12:26 2.3M chainHg38.sql 15-Jun-2020 13:06 1.7K chainHg38.txt.gz 15-Jun-2020 13:06 56M chainHg38Link.sql 15-Jun-2020 13:07 1.5K chainHg38Link.txt.gz 15-Jun-2020 13:07 164M netHg38.sql 15-Jun-2020 13:09 2.1K netHg38.txt.gz 15-Jun-2020 13:09 5.9M genscan.sql 15-Jun-2020 13:18 1.7K genscan.txt.gz 15-Jun-2020 13:18 2.8M chainMm10.sql 15-Jun-2020 17:21 1.7K chainMm10.txt.gz 15-Jun-2020 17:21 67M chainMm10Link.sql 15-Jun-2020 17:25 1.5K chainMm10Link.txt.gz 15-Jun-2020 17:25 524M netMm10.sql 15-Jun-2020 17:28 2.1K netMm10.txt.gz 15-Jun-2020 17:28 75M all_mrna.sql 16-Jun-2020 17:21 2.1K all_mrna.txt.gz 16-Jun-2020 17:21 14K refFlat.sql 16-Jun-2020 17:28 1.7K refFlat.txt.gz 16-Jun-2020 17:28 7.1K refGene.sql 16-Jun-2020 17:28 1.9K refGene.txt.gz 16-Jun-2020 17:28 8.0K xenoRefGene.sql 16-Jun-2020 17:28 1.9K xenoRefGene.txt.gz 16-Jun-2020 17:28 12M refSeqAli.sql 16-Jun-2020 17:28 2.1K refSeqAli.txt.gz 16-Jun-2020 17:28 8.3K xenoRefFlat.sql 16-Jun-2020 17:28 1.7K xenoRefFlat.txt.gz 16-Jun-2020 17:28 10M xenoRefSeqAli.sql 16-Jun-2020 17:28 2.1K xenoRefSeqAli.txt.gz 16-Jun-2020 17:28 20M gbLoaded.sql 16-Jun-2020 17:31 1.6K gbLoaded.txt.gz 16-Jun-2020 17:31 392 mrnaOrientInfo.sql 16-Jun-2020 17:31 1.8K mrnaOrientInfo.txt.gz 16-Jun-2020 17:31 8.7K crisprAllRanges.sql 21-Jun-2020 18:45 1.5K crisprAllRanges.txt.gz 21-Jun-2020 18:45 9.6K crisprAllTargets.sql 22-Jun-2020 01:13 1.3K crisprAllTargets.txt.gz 22-Jun-2020 01:13 69 history.sql 22-Jun-2020 01:39 1.6K history.txt.gz 22-Jun-2020 01:39 896 tableDescriptions.sql 07-Jul-2020 02:04 1.4K tableDescriptions.txt.gz 07-Jul-2020 02:04 6.0K hgFindSpec.sql 25-Oct-2020 08:17 1.7K hgFindSpec.txt.gz 25-Oct-2020 08:17 1.0K trackDb.sql 25-Oct-2020 08:17 2.0K trackDb.txt.gz 25-Oct-2020 08:17 35K tableList.sql 29-Nov-2020 03:06 1.5K tableList.txt.gz 29-Nov-2020 03:06 2.9K bigFiles.sql 29-Nov-2020 03:06 1.4K bigFiles.txt.gz 29-Nov-2020 03:06 119