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.

---------------------------------------------------------------
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 - gap.sql 2020-06-12 10:45 1.6K gold.sql 2020-06-12 10:45 1.7K gold.txt.gz 2020-06-12 10:45 66K gap.txt.gz 2020-06-12 10:45 11K cpgIslandExtUnmasked.sql 2020-06-12 11:36 1.7K cpgIslandExtUnmasked.txt.gz 2020-06-12 11:36 1.0M chromAlias.sql 2020-06-12 12:33 1.4K chromAlias.txt.gz 2020-06-12 12:33 93K simpleRepeat.sql 2020-06-12 17:08 1.9K simpleRepeat.txt.gz 2020-06-12 17:08 26M cytoBandIdeo.sql 2020-06-12 17:27 1.5K cytoBandIdeo.txt.gz 2020-06-12 17:27 27K gc5BaseBw.sql 2020-06-12 17:27 1.3K grp.sql 2020-06-12 17:27 1.3K ucscToINSDC.sql 2020-06-12 17:27 1.4K ucscToRefSeq.sql 2020-06-12 17:27 1.4K gc5BaseBw.txt.gz 2020-06-12 17:27 66 grp.txt.gz 2020-06-12 17:27 213 ucscToRefSeq.txt.gz 2020-06-12 17:27 37K ucscToINSDC.txt.gz 2020-06-12 17:27 39K chromInfo.sql 2020-06-12 18:00 1.4K chromInfo.txt.gz 2020-06-12 18:00 27K rmsk.sql 2020-06-12 18:21 1.9K rmsk.txt.gz 2020-06-12 18:21 139M nestedRepeats.sql 2020-06-12 18:23 1.9K nestedRepeats.txt.gz 2020-06-12 18:23 18M windowmaskerSdust.sql 2020-06-12 19:56 1.5K windowmaskerSdust.txt.gz 2020-06-12 19:56 145M microsat.sql 2020-06-13 10:04 1.5K microsat.txt.gz 2020-06-13 10:04 304K ncbiRefSeq.sql 2020-06-13 10:16 1.9K ncbiRefSeqCurated.sql 2020-06-13 10:16 2.0K ncbiRefSeq.txt.gz 2020-06-13 10:16 4.0M ncbiRefSeqCurated.txt.gz 2020-06-13 10:16 8.5K ncbiRefSeqPredicted.sql 2020-06-13 10:16 2.0K ncbiRefSeqPredicted.txt.gz 2020-06-13 10:16 4.0M ncbiRefSeqLink.sql 2020-06-13 10:16 2.0K ncbiRefSeqLink.txt.gz 2020-06-13 10:16 2.2M ncbiRefSeqPsl.sql 2020-06-13 10:16 2.1K ncbiRefSeqPsl.txt.gz 2020-06-13 10:16 5.7M ncbiRefSeqOther.sql 2020-06-13 15:32 1.3K ncbiRefSeqPepTable.sql 2020-06-13 15:32 1.4K ncbiRefSeqOther.txt.gz 2020-06-13 15:32 75 ncbiRefSeqPepTable.txt.gz 2020-06-13 15:32 12M extNcbiRefSeq.sql 2020-06-13 15:42 1.4K extNcbiRefSeq.txt.gz 2020-06-13 15:42 91 ncbiRefSeqCds.sql 2020-06-13 15:42 1.3K seqNcbiRefSeq.sql 2020-06-13 15:42 1.5K seqNcbiRefSeq.txt.gz 2020-06-13 15:42 1.3M ncbiRefSeqCds.txt.gz 2020-06-13 15:42 500K cpgIslandExt.sql 2020-06-15 09:12 1.7K cpgIslandExt.txt.gz 2020-06-15 09:12 625K augustusGene.sql 2020-06-15 12:26 1.9K augustusGene.txt.gz 2020-06-15 12:26 2.3M chainHg38.sql 2020-06-15 13:06 1.7K chainHg38.txt.gz 2020-06-15 13:06 56M chainHg38Link.sql 2020-06-15 13:07 1.5K chainHg38Link.txt.gz 2020-06-15 13:07 164M netHg38.sql 2020-06-15 13:09 2.1K netHg38.txt.gz 2020-06-15 13:09 5.9M genscan.sql 2020-06-15 13:18 1.7K genscan.txt.gz 2020-06-15 13:18 2.8M chainMm10.sql 2020-06-15 17:21 1.7K chainMm10.txt.gz 2020-06-15 17:21 67M chainMm10Link.sql 2020-06-15 17:25 1.5K chainMm10Link.txt.gz 2020-06-15 17:25 524M netMm10.sql 2020-06-15 17:28 2.1K netMm10.txt.gz 2020-06-15 17:28 75M all_mrna.sql 2020-06-16 17:21 2.1K all_mrna.txt.gz 2020-06-16 17:21 14K refFlat.sql 2020-06-16 17:28 1.7K refGene.sql 2020-06-16 17:28 1.9K refGene.txt.gz 2020-06-16 17:28 8.0K refFlat.txt.gz 2020-06-16 17:28 7.1K xenoRefGene.sql 2020-06-16 17:28 1.9K xenoRefGene.txt.gz 2020-06-16 17:28 12M refSeqAli.sql 2020-06-16 17:28 2.1K xenoRefFlat.sql 2020-06-16 17:28 1.7K xenoRefFlat.txt.gz 2020-06-16 17:28 10M refSeqAli.txt.gz 2020-06-16 17:28 8.3K xenoRefSeqAli.sql 2020-06-16 17:28 2.1K xenoRefSeqAli.txt.gz 2020-06-16 17:28 20M gbLoaded.sql 2020-06-16 17:31 1.6K mrnaOrientInfo.sql 2020-06-16 17:31 1.8K mrnaOrientInfo.txt.gz 2020-06-16 17:31 8.7K gbLoaded.txt.gz 2020-06-16 17:31 392 crisprAllRanges.sql 2020-06-21 18:45 1.5K crisprAllRanges.txt.gz 2020-06-21 18:45 9.6K crisprAllTargets.sql 2020-06-22 01:13 1.3K crisprAllTargets.txt.gz 2020-06-22 01:13 69 history.sql 2020-06-22 01:39 1.6K history.txt.gz 2020-06-22 01:39 896 chainMm39.sql 2020-11-24 11:33 1.7K chainMm39.txt.gz 2020-11-24 11:33 92M chainMm39Link.sql 2020-11-24 11:37 1.6K chainMm39Link.txt.gz 2020-11-24 11:37 557M netMm39.sql 2020-11-24 11:41 2.1K netMm39.txt.gz 2020-11-24 11:41 83M tableDescriptions.sql 2021-03-13 06:37 1.4K tableDescriptions.txt.gz 2021-03-13 06:37 6.1K trackDb.sql 2021-06-10 16:54 2.1K trackDb.txt.gz 2021-06-10 16:54 37K hgFindSpec.sql 2021-06-10 16:54 1.8K hgFindSpec.txt.gz 2021-06-10 16:54 1.0K bigFiles.sql 2021-06-13 03:04 1.4K bigFiles.txt.gz 2021-06-13 03:04 119 tableList.sql 2021-06-13 03:04 1.6K tableList.txt.gz 2021-06-13 03:04 3.0K