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;'

-----------------------------------------------------------------------------
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 2018-11-01 17:05 66 ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75 extNcbiRefSeq.txt.gz 2020-05-10 03:28 91 bigFiles.txt.gz 2024-11-03 03:05 95 grp.txt.gz 2018-11-01 17:05 213 history.txt.gz 2018-11-01 17:01 853 hgFindSpec.txt.gz 2024-07-25 09:34 1.1K gc5BaseBw.sql 2018-11-01 17:05 1.3K ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K grp.sql 2018-11-01 17:05 1.3K ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K chromInfo.sql 2018-11-01 17:05 1.4K bigFiles.sql 2024-11-03 03:05 1.4K chromAlias.sql 2018-11-01 17:05 1.4K ucscToINSDC.sql 2018-11-01 17:06 1.4K ucscToRefSeq.sql 2018-11-01 17:06 1.4K extNcbiRefSeq.sql 2020-05-10 03:28 1.4K tableDescriptions.sql 2024-11-02 02:04 1.5K microsat.sql 2018-11-01 17:06 1.5K windowmaskerSdust.sql 2018-11-01 17:06 1.5K cytoBandIdeo.sql 2018-11-01 17:05 1.5K chainHg38Link.sql 2018-11-01 17:01 1.5K chainMm10Link.sql 2018-11-01 17:02 1.5K seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K history.sql 2018-11-01 17:01 1.6K tableList.sql 2024-11-03 03:05 1.6K gap.sql 2018-11-01 17:05 1.6K gold.sql 2018-11-01 17:06 1.7K genscan.sql 2018-11-01 17:06 1.7K cpgIslandExt.sql 2018-11-01 17:05 1.7K chainHg38.sql 2018-11-01 17:01 1.7K chainMm10.sql 2018-11-01 17:02 1.7K refFlat.sql 2018-11-01 17:05 1.7K cpgIslandExtUnmasked.sql 2018-11-01 17:05 1.7K xenoRefFlat.sql 2018-11-01 17:06 1.7K estOrientInfo.sql 2018-11-01 17:05 1.8K mrnaOrientInfo.sql 2018-11-01 17:06 1.8K hgFindSpec.sql 2024-07-25 09:34 1.8K rmsk.sql 2018-11-01 17:05 1.9K refGene.sql 2018-11-01 17:05 1.9K simpleRepeat.sql 2018-11-01 17:06 1.9K ncbiRefSeq.sql 2020-05-10 03:28 1.9K nestedRepeats.sql 2018-11-01 17:00 1.9K xenoRefGene.sql 2018-11-01 17:06 1.9K augustusGene.sql 2018-11-01 17:00 1.9K ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K trackDb.sql 2024-07-25 09:34 2.1K netHg38.sql 2018-11-01 17:00 2.1K netMm10.sql 2018-11-01 17:01 2.1K all_est.sql 2018-11-01 17:00 2.1K all_mrna.sql 2018-11-01 17:00 2.1K intronEst.sql 2018-11-01 17:06 2.1K refSeqAli.sql 2018-11-01 17:05 2.1K ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K xenoRefSeqAli.sql 2018-11-01 17:07 2.1K tableList.txt.gz 2024-11-03 03:05 3.0K tableDescriptions.txt.gz 2024-11-02 02:04 6.1K gap.txt.gz 2018-11-01 17:05 8.7K cytoBandIdeo.txt.gz 2018-11-01 17:05 33K chromInfo.txt.gz 2018-11-01 17:05 36K ucscToRefSeq.txt.gz 2018-11-01 17:06 47K ucscToINSDC.txt.gz 2018-11-01 17:06 51K chromAlias.txt.gz 2018-11-01 17:05 54K trackDb.txt.gz 2024-07-25 09:34 64K gold.txt.gz 2018-11-01 17:06 80K mrnaOrientInfo.txt.gz 2018-11-01 17:06 150K microsat.txt.gz 2018-11-01 17:06 239K ncbiRefSeqCds.txt.gz 2020-05-10 03:28 338K refFlat.txt.gz 2018-11-01 17:05 359K ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 366K refGene.txt.gz 2018-11-01 17:05 385K refSeqAli.txt.gz 2018-11-01 17:05 398K all_mrna.txt.gz 2018-11-01 17:00 531K cpgIslandExt.txt.gz 2018-11-01 17:05 591K estOrientInfo.txt.gz 2018-11-01 17:05 648K cpgIslandExtUnmasked.txt.gz 2018-11-01 17:05 862K seqNcbiRefSeq.txt.gz 2020-05-10 03:28 881K intronEst.txt.gz 2018-11-01 17:06 1.3M ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.6M all_est.txt.gz 2018-11-01 17:00 2.1M augustusGene.txt.gz 2018-11-01 17:00 2.3M genscan.txt.gz 2018-11-01 17:06 2.8M ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 3.1M ncbiRefSeq.txt.gz 2020-05-10 03:28 3.3M ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 4.2M ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 9.3M netHg38.txt.gz 2018-11-01 17:01 11M nestedRepeats.txt.gz 2018-11-01 17:00 18M xenoRefSeqAli.txt.gz 2018-11-01 17:07 20M xenoRefFlat.txt.gz 2018-11-01 17:06 20M xenoRefGene.txt.gz 2018-11-01 17:06 22M chainHg38.txt.gz 2018-11-01 17:01 23M simpleRepeat.txt.gz 2018-11-01 17:06 28M chainMm10.txt.gz 2018-11-01 17:02 60M netMm10.txt.gz 2018-11-01 17:02 72M rmsk.txt.gz 2018-11-01 17:05 141M windowmaskerSdust.txt.gz 2018-11-01 17:06 146M chainHg38Link.txt.gz 2018-11-01 17:01 157M chainMm10Link.txt.gz 2018-11-01 17:03 503M