This directory contains a dump of the UCSC genome annotation database for the
    Jun. 2015 (MPI-EVA AptMant0/aptMan1) assembly of the brown kiwi genome
    (aptMan1, Max-Plank Institute for Evolutionary Anthropology AptMant0) .

The annotations were generated by UCSC and collaborators worldwide.

For more information about this assembly, please note the NCBI resources:
    http://www.ncbi.nlm.nih.gov/genome/10907
    http://www.ncbi.nlm.nih.gov/assembly/GCF_001039765.1
    http://www.ncbi.nlm.nih.gov/bioproject/287231

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=aptMan1
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.cse.ucsc.edu, then go to
the directory goldenPath/aptMan1/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.cse.ucsc.edu/goldenPath/aptMan1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/aptMan1/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/aptMan1/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/aptMan1/database/gc5BaseBw.txt.gz' 
        -O gc5BaseBw.txt.gz

Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.cse.ucsc.edu/gbdb/

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 aptMan1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql aptMan1 --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_mrna.sql 2020-05-05 21:19 2.1K all_mrna.txt.gz 2020-05-05 21:19 514 augustusGene.sql 2016-03-18 11:11 1.9K augustusGene.txt.gz 2016-03-18 11:11 1.5M bigFiles.sql 2022-06-26 03:10 1.4K bigFiles.txt.gz 2022-06-26 03:10 69 chromInfo.sql 2016-03-18 11:11 1.4K chromInfo.txt.gz 2016-03-18 11:11 124K cpgIslandExt.sql 2016-03-18 11:11 1.7K cpgIslandExt.txt.gz 2016-03-18 11:11 1.1M cpgIslandExtUnmasked.sql 2016-03-18 11:11 1.7K cpgIslandExtUnmasked.txt.gz 2016-03-18 11:11 1.2M cytoBandIdeo.sql 2016-03-18 11:11 1.5K cytoBandIdeo.txt.gz 2016-03-18 11:11 121K gap.sql 2016-03-18 11:11 1.6K gap.txt.gz 2016-03-18 11:11 2.4M gbLoaded.sql 2020-08-18 06:44 1.6K gbLoaded.txt.gz 2020-08-18 06:44 46K gc5BaseBw.sql 2016-03-18 11:11 1.3K gc5BaseBw.txt.gz 2016-03-18 11:11 66 genscan.sql 2016-03-18 11:11 1.7K genscan.txt.gz 2016-03-18 11:11 1.9M genscanSubopt.sql 2016-03-18 11:11 1.6K genscanSubopt.txt.gz 2016-03-18 11:11 4.8M gold.sql 2016-03-18 11:11 1.7K gold.txt.gz 2016-03-18 11:11 3.3M grp.sql 2016-03-18 11:11 1.3K grp.txt.gz 2016-03-18 11:11 213 hgFindSpec.sql 2021-08-02 14:26 1.8K hgFindSpec.txt.gz 2021-08-02 14:26 536 history.sql 2016-03-18 11:11 1.6K history.txt.gz 2016-03-18 11:11 377 microsat.sql 2016-03-18 11:11 1.5K microsat.txt.gz 2016-03-18 11:11 47K mrnaOrientInfo.sql 2020-05-05 21:19 1.8K mrnaOrientInfo.txt.gz 2020-05-05 21:19 210 refFlat.sql 2020-05-05 16:36 1.7K refFlat.txt.gz 2020-05-05 16:36 140 refGene.sql 2020-05-05 16:36 1.9K refGene.txt.gz 2020-05-05 16:36 158 refSeqAli.sql 2016-03-18 11:11 2.1K refSeqAli.txt.gz 2016-03-18 11:11 161 rmsk.sql 2016-03-18 11:11 1.9K rmsk.txt.gz 2016-03-18 11:11 12M simpleRepeat.sql 2016-03-18 11:11 1.9K simpleRepeat.txt.gz 2016-03-18 11:11 24M tableDescriptions.sql 2019-07-21 03:41 1.4K tableDescriptions.txt.gz 2019-07-21 03:41 4.1K tableList.sql 2022-06-26 03:10 1.6K tableList.txt.gz 2022-06-26 03:10 1.8K trackDb.sql 2021-08-02 14:26 2.1K trackDb.txt.gz 2021-08-02 14:26 23K windowmaskerSdust.sql 2016-03-18 11:11 1.5K windowmaskerSdust.txt.gz 2016-03-18 11:11 68M xenoRefFlat.sql 2020-08-18 06:44 1.7K xenoRefFlat.txt.gz 2020-08-18 06:44 28M xenoRefGene.sql 2020-08-18 06:44 1.9K xenoRefGene.txt.gz 2020-08-18 06:44 30M xenoRefSeqAli.sql 2020-08-18 06:44 2.1K xenoRefSeqAli.txt.gz 2020-08-18 06:44 27M