This directory contains a dump of the UCSC genome annotation database for
the Aug. 2011 (SGSC Sscrofa10.2/susScr3) assembly of the pig genome (susScr3, SGSC Sscrofa10.2 (NCBI project 13421, GCA_000003025.4, WGS AEMK01)).
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/84
    http://www.ncbi.nlm.nih.gov/genome/assembly/304498
    http://www.ncbi.nlm.nih.gov/bioproject/13421

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=susScr3
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/susScr3/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/susScr3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/susScr3/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr3/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr3/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 susScr3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql susScr3 --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.

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All the files and tables in this directory are freely usable for any purpose.
-----------------------------------------------------------------------------
      Name                        Last modified      Size  Description
Parent Directory - all_est.sql 2015-04-06 07:36 2.1K all_est.txt.gz 2015-04-06 07:36 57M all_mrna.sql 2020-09-02 07:33 2.1K all_mrna.txt.gz 2020-09-02 07:33 2.7M animalQtl.sql 2014-06-30 03:14 1.5K animalQtl.txt.gz 2014-06-30 03:14 94K augustusGene.sql 2015-07-26 17:28 1.9K augustusGene.txt.gz 2015-07-26 17:28 2.3M bigFiles.sql 2024-10-06 03:36 1.4K bigFiles.txt.gz 2024-10-06 03:36 94 chainMm10.sql 2012-11-16 12:35 1.7K chainMm10.txt.gz 2012-11-16 12:35 63M chainMm10Link.sql 2012-11-16 12:32 1.5K chainMm10Link.txt.gz 2012-11-16 12:33 509M chainMm39.sql 2020-11-24 20:26 1.7K chainMm39.txt.gz 2020-11-24 20:26 53M chainMm39Link.sql 2020-11-24 20:30 1.6K chainMm39Link.txt.gz 2020-11-24 20:30 479M chromAlias.sql 2018-02-18 08:48 1.4K chromAlias.txt.gz 2018-02-18 08:48 48K chromInfo.sql 2012-11-16 12:38 1.4K chromInfo.txt.gz 2012-11-16 12:38 29K cpgIslandExt.sql 2012-11-16 12:35 1.7K cpgIslandExt.txt.gz 2012-11-16 12:35 917K cpgIslandExtUnmasked.sql 2014-06-01 20:00 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 20:00 1.4M cytoBandIdeo.sql 2013-04-28 22:14 1.5K cytoBandIdeo.txt.gz 2013-04-28 22:14 26K ensGene.sql 2016-11-20 09:48 1.9K ensGene.txt.gz 2016-11-20 09:48 2.3M ensGtp.sql 2016-11-20 09:45 1.4K ensGtp.txt.gz 2016-11-20 09:45 283K ensPep.sql 2016-11-20 09:45 1.3K ensPep.txt.gz 2016-11-20 09:45 6.5M ensemblSource.sql 2016-11-20 09:45 1.4K ensemblSource.txt.gz 2016-11-20 09:45 93K ensemblToGeneName.sql 2016-11-20 09:48 1.4K ensemblToGeneName.txt.gz 2016-11-20 09:48 133K estOrientInfo.sql 2015-04-06 07:32 1.8K estOrientInfo.txt.gz 2015-04-06 07:32 18M extNcbiRefSeq.sql 2018-08-14 02:28 1.5K extNcbiRefSeq.txt.gz 2018-08-14 02:28 91 gap.sql 2012-11-16 12:32 1.6K gap.txt.gz 2012-11-16 12:32 1.7M gbLoaded.sql 2020-09-02 07:33 1.6K gbLoaded.txt.gz 2020-09-02 07:33 82K gc5BaseBw.sql 2012-11-16 12:36 1.3K gc5BaseBw.txt.gz 2012-11-16 12:36 63 genscan.sql 2012-11-16 12:38 1.7K genscan.txt.gz 2012-11-16 12:38 3.0M gold.sql 2012-11-16 12:40 1.7K gold.txt.gz 2012-11-16 12:40 2.4M grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.sql 2024-07-25 09:34 1.8K hgFindSpec.txt.gz 2024-07-25 09:34 1.5K history.sql 2012-11-16 12:38 1.6K history.txt.gz 2012-11-16 12:38 612 intronEst.sql 2015-04-06 07:30 2.1K intronEst.txt.gz 2015-04-06 07:30 31M microsat.sql 2015-08-24 02:15 1.5K microsat.txt.gz 2015-08-24 02:15 399K mrnaOrientInfo.sql 2020-09-02 07:33 1.8K mrnaOrientInfo.txt.gz 2020-09-02 07:33 757K ncbiRefSeq.sql 2018-02-09 13:52 2.0K ncbiRefSeq.txt.gz 2018-02-09 13:52 3.5M ncbiRefSeqCds.sql 2018-08-14 02:28 1.4K ncbiRefSeqCds.txt.gz 2018-08-14 02:28 325K ncbiRefSeqCurated.sql 2018-02-09 13:52 2.0K ncbiRefSeqCurated.txt.gz 2018-02-09 13:52 377K ncbiRefSeqLink.sql 2018-02-09 13:52 2.0K ncbiRefSeqLink.txt.gz 2018-02-09 13:52 1.8M ncbiRefSeqOther.sql 2018-08-14 02:28 1.3K ncbiRefSeqOther.txt.gz 2018-08-14 02:28 75 ncbiRefSeqPepTable.sql 2018-08-14 02:28 1.4K ncbiRefSeqPepTable.txt.gz 2018-08-14 02:28 9.3M ncbiRefSeqPredicted.sql 2018-02-09 13:52 2.0K ncbiRefSeqPredicted.txt.gz 2018-02-09 13:52 3.2M ncbiRefSeqPsl.sql 2018-02-09 13:52 2.1K ncbiRefSeqPsl.txt.gz 2018-02-09 13:52 4.4M nestedRepeats.sql 2012-11-16 12:39 1.9K nestedRepeats.txt.gz 2012-11-16 12:39 14M netMm10.sql 2012-11-16 12:31 2.1K netMm10.txt.gz 2012-11-16 12:31 58M netMm39.sql 2020-11-24 20:32 2.1K netMm39.txt.gz 2020-11-24 20:32 58M pubsBingBlat.sql 2014-01-26 19:12 2.4K pubsBingBlat.txt.gz 2014-01-26 19:12 1.0M pubsBingBlatPsl.sql 2014-01-26 19:12 2.2K pubsBingBlatPsl.txt.gz 2014-01-26 19:12 756K refFlat.sql 2020-09-02 07:33 1.7K refFlat.txt.gz 2020-09-02 07:33 402K refGene.sql 2020-09-02 07:33 1.9K refGene.txt.gz 2020-09-02 07:33 442K refSeqAli.sql 2020-09-02 07:33 2.1K refSeqAli.txt.gz 2020-09-02 07:33 458K rmsk.sql 2012-11-16 12:36 1.9K rmsk.txt.gz 2012-11-16 12:36 124M seqNcbiRefSeq.sql 2018-08-14 02:28 1.6K seqNcbiRefSeq.txt.gz 2018-08-14 02:28 1.0M simpleRepeat.sql 2012-11-16 12:34 1.9K simpleRepeat.txt.gz 2012-11-16 12:34 16M snp138.sql 2014-03-02 04:14 2.9K snp138.txt.gz 2014-03-02 04:15 369M snp138CodingDbSnp.sql 2014-03-02 04:17 1.7K snp138CodingDbSnp.txt.gz 2014-03-02 04:17 3.4M snp138ExceptionDesc.sql 2014-03-02 04:17 1.4K snp138ExceptionDesc.txt.gz 2014-03-02 04:17 1.0K snp138Mult.sql 2014-03-02 04:17 2.9K snp138Mult.txt.gz 2014-03-02 04:17 1.7M snp138Seq.sql 2014-03-02 04:17 1.3K snp138Seq.txt.gz 2014-03-02 04:17 170M tableDescriptions.sql 2024-10-05 02:03 1.5K tableDescriptions.txt.gz 2024-10-05 02:03 8.5K tableList.sql 2024-10-06 03:36 1.6K tableList.txt.gz 2024-10-06 03:36 4.5K trackDb.sql 2024-07-25 09:34 2.1K trackDb.txt.gz 2024-07-25 09:34 85K ucscToINSDC.sql 2013-09-15 19:49 1.4K ucscToINSDC.txt.gz 2013-09-15 19:49 37K ucscToRefSeq.sql 2018-02-18 08:48 1.4K ucscToRefSeq.txt.gz 2018-02-18 08:48 39K windowmaskerSdust.sql 2012-11-16 12:35 1.5K windowmaskerSdust.txt.gz 2012-11-16 12:35 126M xenoMrna.sql 2020-09-02 07:33 2.1K xenoMrna.txt.gz 2020-09-02 07:33 385M xenoRefFlat.sql 2020-09-02 07:33 1.7K xenoRefFlat.txt.gz 2020-09-02 07:33 36M xenoRefGene.sql 2020-09-02 07:33 2.0K xenoRefGene.txt.gz 2020-09-02 07:33 40M xenoRefSeqAli.sql 2020-09-02 07:33 2.1K xenoRefSeqAli.txt.gz 2020-09-02 07:33 41M