This directory contains a dump of the UCSC genome annotation database for the
    Aug. 2012 (ISGC Oar_v3.1/oviAri3) assembly of the sheep genome
    (oviAri3, International Sheep Genome Consortium) .

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/83
    http://www.ncbi.nlm.nih.gov/genome/assembly/457978
    http://www.ncbi.nlm.nih.gov/bioproject/179263

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=oviAri3
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.cse.ucsc.edu, then go to
the directory goldenPath/oviAri3/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/oviAri3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/oviAri3/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/oviAri3/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/oviAri3/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 oviAri3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql oviAri3 --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 - chainHg19Link.sql 2013-08-30 12:21 1.5K chainHg19Link.txt.gz 2013-08-30 12:22 816M chromInfo.sql 2013-08-30 12:31 1.4K chromInfo.txt.gz 2013-08-30 12:31 34K genscan.sql 2013-08-30 12:31 1.7K genscan.txt.gz 2013-08-30 12:31 3.0M history.sql 2013-08-30 12:31 1.6K history.txt.gz 2013-08-30 12:31 392 netHg19.sql 2013-08-30 12:31 2.1K netHg19.txt.gz 2013-08-30 12:31 66M gap.sql 2013-08-30 12:31 1.6K gap.txt.gz 2013-08-30 12:31 1.7M rmsk.sql 2013-08-30 12:31 1.9K rmsk.txt.gz 2013-08-30 12:32 135M genscanSubopt.sql 2013-08-30 12:32 1.6K genscanSubopt.txt.gz 2013-08-30 12:32 5.8M cpgIslandExt.sql 2013-08-30 12:32 1.7K cpgIslandExt.txt.gz 2013-08-30 12:32 810K gold.sql 2013-08-30 12:32 1.7K gold.txt.gz 2013-08-30 12:32 2.3M simpleRepeat.sql 2013-08-30 12:32 1.9K simpleRepeat.txt.gz 2013-08-30 12:32 17M nestedRepeats.sql 2013-08-30 12:32 1.9K nestedRepeats.txt.gz 2013-08-30 12:32 14M chainHg19.sql 2013-08-30 12:33 1.7K chainHg19.txt.gz 2013-08-30 12:33 189M gc5BaseBw.sql 2013-08-30 12:33 1.3K gc5BaseBw.txt.gz 2013-08-30 12:33 63 windowmaskerSdust.sql 2013-08-30 12:33 1.5K windowmaskerSdust.txt.gz 2013-08-30 12:34 121M grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 cpgIslandExtUnmasked.sql 2014-06-01 18:04 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 18:04 918K animalQtl.sql 2014-06-30 01:24 1.5K animalQtl.txt.gz 2014-06-30 01:24 8.9K cytoBandIdeo.sql 2014-12-14 19:18 1.5K cytoBandIdeo.txt.gz 2014-12-14 19:18 32K augustusGene.sql 2015-07-26 17:21 1.9K augustusGene.txt.gz 2015-07-26 17:21 2.2M microsat.sql 2015-08-23 23:18 1.5K microsat.txt.gz 2015-08-23 23:18 301K all_est.sql 2016-05-15 11:01 2.1K all_est.txt.gz 2016-05-15 11:01 13M estOrientInfo.sql 2016-05-15 11:01 1.8K estOrientInfo.txt.gz 2016-05-15 11:01 3.8M intronEst.sql 2016-05-15 11:02 2.1K intronEst.txt.gz 2016-05-15 11:02 8.1M ncbiRefSeq.sql 2018-02-09 13:49 2.0K ncbiRefSeq.txt.gz 2018-02-09 13:49 3.3M ncbiRefSeqCurated.sql 2018-02-09 13:49 2.0K ncbiRefSeqCurated.txt.gz 2018-02-09 13:49 70K ncbiRefSeqPredicted.sql 2018-02-09 13:49 2.0K ncbiRefSeqPredicted.txt.gz 2018-02-09 13:49 3.2M ncbiRefSeqLink.sql 2018-02-09 13:49 2.0K ncbiRefSeqLink.txt.gz 2018-02-09 13:49 1.6M ncbiRefSeqPsl.sql 2018-02-09 13:49 2.1K ncbiRefSeqPsl.txt.gz 2018-02-09 13:49 4.4M chromAlias.sql 2018-02-18 07:59 1.4K chromAlias.txt.gz 2018-02-18 07:59 61K ucscToRefSeq.sql 2018-02-18 07:59 1.4K ucscToRefSeq.txt.gz 2018-02-18 07:59 47K extNcbiRefSeq.sql 2018-08-14 02:29 1.5K extNcbiRefSeq.txt.gz 2018-08-14 02:29 91 ncbiRefSeqCds.sql 2018-08-14 02:29 1.4K ncbiRefSeqCds.txt.gz 2018-08-14 02:29 331K ncbiRefSeqOther.sql 2018-08-14 02:29 1.3K ncbiRefSeqOther.txt.gz 2018-08-14 02:29 75 ncbiRefSeqPepTable.sql 2018-08-14 02:29 1.4K ncbiRefSeqPepTable.txt.gz 2018-08-14 02:29 8.5M seqNcbiRefSeq.sql 2018-08-14 02:29 1.6K seqNcbiRefSeq.txt.gz 2018-08-14 02:29 948K all_mrna.sql 2020-08-22 15:54 2.1K xenoMrna.sql 2020-08-22 15:54 2.1K all_mrna.txt.gz 2020-08-22 15:54 215K xenoMrna.txt.gz 2020-08-22 15:54 223M gbLoaded.sql 2020-08-22 16:33 1.6K mrnaOrientInfo.sql 2020-08-22 16:33 1.8K refFlat.sql 2020-08-22 16:33 1.7K refGene.sql 2020-08-22 16:33 1.9K refSeqAli.sql 2020-08-22 16:33 2.1K xenoRefFlat.sql 2020-08-22 16:33 1.7K xenoRefGene.sql 2020-08-22 16:33 1.9K xenoRefSeqAli.sql 2020-08-22 16:33 2.1K refGene.txt.gz 2020-08-22 16:33 82K refFlat.txt.gz 2020-08-22 16:33 74K xenoRefGene.txt.gz 2020-08-22 16:33 26M xenoRefFlat.txt.gz 2020-08-22 16:33 24M mrnaOrientInfo.txt.gz 2020-08-22 16:33 80K refSeqAli.txt.gz 2020-08-22 16:33 86K xenoRefSeqAli.txt.gz 2020-08-22 16:33 26M gbLoaded.txt.gz 2020-08-22 16:33 42K ensGene.sql 2021-05-25 14:40 1.9K ensGene.txt.gz 2021-05-25 14:40 2.3M ensGtp.sql 2021-05-25 14:40 1.4K ensGtp.txt.gz 2021-05-25 14:40 256K ensemblToGeneName.sql 2021-05-25 14:40 1.4K ensemblToGeneName.txt.gz 2021-05-25 14:40 14K ensemblSource.sql 2021-05-25 14:41 1.4K ensemblSource.txt.gz 2021-05-25 14:41 75K ensPep.sql 2021-05-25 14:41 1.3K ensPep.txt.gz 2021-05-25 14:41 6.3M tableDescriptions.sql 2021-08-07 06:33 1.4K tableDescriptions.txt.gz 2021-08-07 06:33 6.4K trackDb.sql 2021-12-27 12:19 2.1K trackDb.txt.gz 2021-12-27 12:19 45K hgFindSpec.sql 2021-12-27 12:19 1.8K hgFindSpec.txt.gz 2021-12-27 12:19 1.2K bigFiles.sql 2022-08-07 03:10 1.4K bigFiles.txt.gz 2022-08-07 03:10 94 tableList.sql 2022-08-07 03:10 1.6K tableList.txt.gz 2022-08-07 03:10 3.2K