This directory contains a dump of the UCSC genome annotation database for the
    Jan. 2018 (Susie_PABv2/ponAbe3) assembly of the orangutan genome
    (ponAbe3, 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/325
    https://www.ncbi.nlm.nih.gov/genome/assembly/1529631
    https://www.ncbi.nlm.nih.gov/bioproject/369439

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=ponAbe3
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/ponAbe3/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/ponAbe3/database/ .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/ponAbe3/database/gc5Base.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/ponAbe3/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/ponAbe3/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 ponAbe3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql ponAbe3 --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 - all_est.sql 2018-11-01 17:00 2.1K all_est.txt.gz 2018-11-01 17:00 2.1M all_mrna.sql 2018-11-01 17:00 2.1K all_mrna.txt.gz 2018-11-01 17:00 531K augustusGene.sql 2018-11-01 17:00 1.9K augustusGene.txt.gz 2018-11-01 17:00 2.3M bigFiles.sql 2021-05-02 03:04 1.4K bigFiles.txt.gz 2021-05-02 03:04 95 chainHg38.sql 2018-11-01 17:01 1.7K chainHg38.txt.gz 2018-11-01 17:01 23M chainHg38Link.sql 2018-11-01 17:01 1.5K chainHg38Link.txt.gz 2018-11-01 17:01 157M chainMm10.sql 2018-11-01 17:02 1.7K chainMm10.txt.gz 2018-11-01 17:02 60M chainMm10Link.sql 2018-11-01 17:02 1.5K chainMm10Link.txt.gz 2018-11-01 17:03 503M chromAlias.sql 2018-11-01 17:05 1.4K chromAlias.txt.gz 2018-11-01 17:05 54K chromInfo.sql 2018-11-01 17:05 1.4K chromInfo.txt.gz 2018-11-01 17:05 36K cpgIslandExt.sql 2018-11-01 17:05 1.7K cpgIslandExt.txt.gz 2018-11-01 17:05 591K cpgIslandExtUnmasked.sql 2018-11-01 17:05 1.7K cpgIslandExtUnmasked.txt.gz 2018-11-01 17:05 862K cytoBandIdeo.sql 2018-11-01 17:05 1.5K cytoBandIdeo.txt.gz 2018-11-01 17:05 33K estOrientInfo.sql 2018-11-01 17:05 1.8K estOrientInfo.txt.gz 2018-11-01 17:05 648K extNcbiRefSeq.sql 2020-05-10 03:28 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:28 91 gap.sql 2018-11-01 17:05 1.6K gap.txt.gz 2018-11-01 17:05 8.7K gc5BaseBw.sql 2018-11-01 17:05 1.3K gc5BaseBw.txt.gz 2018-11-01 17:05 66 genscan.sql 2018-11-01 17:06 1.7K genscan.txt.gz 2018-11-01 17:06 2.8M gold.sql 2018-11-01 17:06 1.7K gold.txt.gz 2018-11-01 17:06 80K grp.sql 2018-11-01 17:05 1.3K grp.txt.gz 2018-11-01 17:05 213 hgFindSpec.sql 2020-12-06 08:20 1.7K hgFindSpec.txt.gz 2020-12-06 08:20 1.0K history.sql 2018-11-01 17:01 1.6K history.txt.gz 2018-11-01 17:01 853 intronEst.sql 2018-11-01 17:06 2.1K intronEst.txt.gz 2018-11-01 17:06 1.3M microsat.sql 2018-11-01 17:06 1.5K microsat.txt.gz 2018-11-01 17:06 239K mrnaOrientInfo.sql 2018-11-01 17:06 1.8K mrnaOrientInfo.txt.gz 2018-11-01 17:06 150K ncbiRefSeq.sql 2020-05-10 03:28 1.9K ncbiRefSeq.txt.gz 2020-05-10 03:28 3.3M ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K ncbiRefSeqCds.txt.gz 2020-05-10 03:28 338K ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 366K ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.6M ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75 ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 9.3M ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 3.1M ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 4.2M nestedRepeats.sql 2018-11-01 17:00 1.9K nestedRepeats.txt.gz 2018-11-01 17:00 18M netHg38.sql 2018-11-01 17:00 2.1K netHg38.txt.gz 2018-11-01 17:01 11M netMm10.sql 2018-11-01 17:01 2.1K netMm10.txt.gz 2018-11-01 17:02 72M refFlat.sql 2018-11-01 17:05 1.7K refFlat.txt.gz 2018-11-01 17:05 359K refGene.sql 2018-11-01 17:05 1.9K refGene.txt.gz 2018-11-01 17:05 385K refSeqAli.sql 2018-11-01 17:05 2.1K refSeqAli.txt.gz 2018-11-01 17:05 398K rmsk.sql 2018-11-01 17:05 1.9K rmsk.txt.gz 2018-11-01 17:05 141M seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:28 881K simpleRepeat.sql 2018-11-01 17:06 1.9K simpleRepeat.txt.gz 2018-11-01 17:06 28M tableDescriptions.sql 2019-07-21 03:43 1.4K tableDescriptions.txt.gz 2019-07-21 03:43 6.1K tableList.sql 2021-05-02 03:04 1.6K tableList.txt.gz 2021-05-02 03:04 3.0K trackDb.sql 2020-12-06 08:20 2.0K trackDb.txt.gz 2020-12-06 08:20 41K ucscToINSDC.sql 2018-11-01 17:06 1.4K ucscToINSDC.txt.gz 2018-11-01 17:06 51K ucscToRefSeq.sql 2018-11-01 17:06 1.4K ucscToRefSeq.txt.gz 2018-11-01 17:06 47K windowmaskerSdust.sql 2018-11-01 17:06 1.5K windowmaskerSdust.txt.gz 2018-11-01 17:06 146M xenoRefFlat.sql 2018-11-01 17:06 1.7K xenoRefFlat.txt.gz 2018-11-01 17:06 20M xenoRefGene.sql 2018-11-01 17:06 1.9K xenoRefGene.txt.gz 2018-11-01 17:06 22M xenoRefSeqAli.sql 2018-11-01 17:07 2.1K xenoRefSeqAli.txt.gz 2018-11-01 17:07 20M