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