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:
    https://www.ncbi.nlm.nih.gov/genome/10729
    https://www.ncbi.nlm.nih.gov/genome/assembly/7133581
    https://www.ncbi.nlm.nih.gov/bioproject/526933
    https://www.ncbi.nlm.nih.gov/biosample/SAMN11123633

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=panPan3
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.soe.ucsc.edu, 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://hgdownload.soe.ucsc.edu/goldenPath/panPan3/database/ .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/panPan3/database/gc5Base.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/panPan3/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/panPan3/database/gc5Base.txt.gz' 
        -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;'

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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 2020-06-12 17:27 66 crisprAllTargets.txt.gz 2020-06-22 01:13 69 ncbiRefSeqOther.txt.gz 2020-06-13 15:32 75 extNcbiRefSeq.txt.gz 2020-06-13 15:42 91 bigFiles.txt.gz 2021-11-28 03:03 119 grp.txt.gz 2020-06-12 17:27 213 gbLoaded.txt.gz 2020-06-16 17:31 392 history.txt.gz 2020-06-22 01:39 896 hgFindSpec.txt.gz 2021-08-02 14:31 1.0K gc5BaseBw.sql 2020-06-12 17:27 1.3K ncbiRefSeqOther.sql 2020-06-13 15:32 1.3K crisprAllTargets.sql 2020-06-22 01:13 1.3K ncbiRefSeqCds.sql 2020-06-13 15:42 1.3K grp.sql 2020-06-12 17:27 1.3K ncbiRefSeqPepTable.sql 2020-06-13 15:32 1.4K bigFiles.sql 2021-11-28 03:03 1.4K chromInfo.sql 2020-06-12 18:00 1.4K chromAlias.sql 2020-06-12 12:33 1.4K tableDescriptions.sql 2021-03-13 06:37 1.4K ucscToINSDC.sql 2020-06-12 17:27 1.4K ucscToRefSeq.sql 2020-06-12 17:27 1.4K extNcbiRefSeq.sql 2020-06-13 15:42 1.4K microsat.sql 2020-06-13 10:04 1.5K crisprAllRanges.sql 2020-06-21 18:45 1.5K windowmaskerSdust.sql 2020-06-12 19:56 1.5K cytoBandIdeo.sql 2020-06-12 17:27 1.5K chainHg38Link.sql 2020-06-15 13:07 1.5K chainMm10Link.sql 2020-06-15 17:25 1.5K seqNcbiRefSeq.sql 2020-06-13 15:42 1.5K chainMm39Link.sql 2020-11-24 11:37 1.6K tableList.sql 2021-11-28 03:03 1.6K history.sql 2020-06-22 01:39 1.6K gbLoaded.sql 2020-06-16 17:31 1.6K gap.sql 2020-06-12 10:45 1.6K gold.sql 2020-06-12 10:45 1.7K genscan.sql 2020-06-15 13:18 1.7K cpgIslandExt.sql 2020-06-15 09:12 1.7K chainHg38.sql 2020-06-15 13:06 1.7K chainMm10.sql 2020-06-15 17:21 1.7K refFlat.sql 2020-06-16 17:28 1.7K cpgIslandExtUnmasked.sql 2020-06-12 11:36 1.7K xenoRefFlat.sql 2020-06-16 17:28 1.7K chainMm39.sql 2020-11-24 11:33 1.7K hgFindSpec.sql 2021-08-02 14:31 1.8K mrnaOrientInfo.sql 2020-06-16 17:31 1.8K rmsk.sql 2020-06-12 18:21 1.9K refGene.sql 2020-06-16 17:28 1.9K simpleRepeat.sql 2020-06-12 17:08 1.9K ncbiRefSeq.sql 2020-06-13 10:16 1.9K nestedRepeats.sql 2020-06-12 18:23 1.9K xenoRefGene.sql 2020-06-16 17:28 1.9K augustusGene.sql 2020-06-15 12:26 1.9K ncbiRefSeqCurated.sql 2020-06-13 10:16 2.0K ncbiRefSeqPredicted.sql 2020-06-13 10:16 2.0K ncbiRefSeqLink.sql 2020-06-13 10:16 2.0K trackDb.sql 2021-08-02 14:31 2.1K netHg38.sql 2020-06-15 13:09 2.1K netMm10.sql 2020-06-15 17:28 2.1K all_mrna.sql 2020-06-16 17:21 2.1K refSeqAli.sql 2020-06-16 17:28 2.1K netMm39.sql 2020-11-24 11:41 2.1K ncbiRefSeqPsl.sql 2020-06-13 10:16 2.1K xenoRefSeqAli.sql 2020-06-16 17:28 2.1K tableList.txt.gz 2021-11-28 03:03 3.0K tableDescriptions.txt.gz 2021-03-13 06:37 6.1K refFlat.txt.gz 2020-06-16 17:28 7.1K refGene.txt.gz 2020-06-16 17:28 8.0K refSeqAli.txt.gz 2020-06-16 17:28 8.3K ncbiRefSeqCurated.txt.gz 2020-06-13 10:16 8.5K mrnaOrientInfo.txt.gz 2020-06-16 17:31 8.7K crisprAllRanges.txt.gz 2020-06-21 18:45 9.6K gap.txt.gz 2020-06-12 10:45 11K all_mrna.txt.gz 2020-06-16 17:21 14K chromInfo.txt.gz 2020-06-12 18:00 27K cytoBandIdeo.txt.gz 2020-06-12 17:27 27K ucscToRefSeq.txt.gz 2020-06-12 17:27 37K trackDb.txt.gz 2021-08-02 14:31 37K ucscToINSDC.txt.gz 2020-06-12 17:27 39K gold.txt.gz 2020-06-12 10:45 66K chromAlias.txt.gz 2020-06-12 12:33 93K microsat.txt.gz 2020-06-13 10:04 304K ncbiRefSeqCds.txt.gz 2020-06-13 15:42 500K cpgIslandExt.txt.gz 2020-06-15 09:12 625K cpgIslandExtUnmasked.txt.gz 2020-06-12 11:36 1.0M seqNcbiRefSeq.txt.gz 2020-06-13 15:42 1.3M ncbiRefSeqLink.txt.gz 2020-06-13 10:16 2.2M augustusGene.txt.gz 2020-06-15 12:26 2.3M genscan.txt.gz 2020-06-15 13:18 2.8M ncbiRefSeqPredicted.txt.gz 2020-06-13 10:16 4.0M ncbiRefSeq.txt.gz 2020-06-13 10:16 4.0M ncbiRefSeqPsl.txt.gz 2020-06-13 10:16 5.7M netHg38.txt.gz 2020-06-15 13:09 5.9M xenoRefFlat.txt.gz 2020-06-16 17:28 10M xenoRefGene.txt.gz 2020-06-16 17:28 12M ncbiRefSeqPepTable.txt.gz 2020-06-13 15:32 12M nestedRepeats.txt.gz 2020-06-12 18:23 18M xenoRefSeqAli.txt.gz 2020-06-16 17:28 20M simpleRepeat.txt.gz 2020-06-12 17:08 26M chainHg38.txt.gz 2020-06-15 13:06 56M chainMm10.txt.gz 2020-06-15 17:21 67M netMm10.txt.gz 2020-06-15 17:28 75M netMm39.txt.gz 2020-11-24 11:41 83M chainMm39.txt.gz 2020-11-24 11:33 92M rmsk.txt.gz 2020-06-12 18:21 139M windowmaskerSdust.txt.gz 2020-06-12 19:56 145M chainHg38Link.txt.gz 2020-06-15 13:07 164M chainMm10Link.txt.gz 2020-06-15 17:25 524M chainMm39Link.txt.gz 2020-11-24 11:37 557M