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.

---------------------------------------------------------------
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;'

-----------------------------------------------------------------------------
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 - netMm10.sql 2012-11-16 12:31 2.1K netMm10.txt.gz 2012-11-16 12:31 58M gap.sql 2012-11-16 12:32 1.6K gap.txt.gz 2012-11-16 12:32 1.7M chainMm10Link.sql 2012-11-16 12:32 1.5K chainMm10Link.txt.gz 2012-11-16 12:33 509M simpleRepeat.sql 2012-11-16 12:34 1.9K simpleRepeat.txt.gz 2012-11-16 12:34 16M windowmaskerSdust.sql 2012-11-16 12:35 1.5K windowmaskerSdust.txt.gz 2012-11-16 12:35 126M chainMm10.sql 2012-11-16 12:35 1.7K chainMm10.txt.gz 2012-11-16 12:35 63M cpgIslandExt.sql 2012-11-16 12:35 1.7K cpgIslandExt.txt.gz 2012-11-16 12:35 917K rmsk.sql 2012-11-16 12:36 1.9K rmsk.txt.gz 2012-11-16 12:36 124M 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 history.sql 2012-11-16 12:38 1.6K history.txt.gz 2012-11-16 12:38 612 chromInfo.sql 2012-11-16 12:38 1.4K chromInfo.txt.gz 2012-11-16 12:38 29K nestedRepeats.sql 2012-11-16 12:39 1.9K nestedRepeats.txt.gz 2012-11-16 12:39 14M gold.sql 2012-11-16 12:40 1.7K gold.txt.gz 2012-11-16 12:40 2.4M cytoBandIdeo.sql 2013-04-28 22:14 1.5K cytoBandIdeo.txt.gz 2013-04-28 22:14 26K ucscToINSDC.sql 2013-09-15 19:49 1.4K ucscToINSDC.txt.gz 2013-09-15 19:49 37K 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 grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 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 cpgIslandExtUnmasked.sql 2014-06-01 20:00 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 20:00 1.4M animalQtl.sql 2014-06-30 03:14 1.5K animalQtl.txt.gz 2014-06-30 03:14 94K intronEst.sql 2015-04-06 07:30 2.1K intronEst.txt.gz 2015-04-06 07:30 31M estOrientInfo.sql 2015-04-06 07:32 1.8K estOrientInfo.txt.gz 2015-04-06 07:32 18M all_est.sql 2015-04-06 07:36 2.1K all_est.txt.gz 2015-04-06 07:36 57M augustusGene.sql 2015-07-26 17:28 1.9K augustusGene.txt.gz 2015-07-26 17:28 2.3M microsat.sql 2015-08-24 02:15 1.5K microsat.txt.gz 2015-08-24 02:15 399K 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 ensGene.sql 2016-11-20 09:48 1.9K ensGene.txt.gz 2016-11-20 09:48 2.3M ensemblToGeneName.sql 2016-11-20 09:48 1.4K ensemblToGeneName.txt.gz 2016-11-20 09:48 133K chromAlias.sql 2018-02-18 08:48 1.4K chromAlias.txt.gz 2018-02-18 08:48 48K ucscToRefSeq.sql 2018-02-18 08:48 1.4K ucscToRefSeq.txt.gz 2018-02-18 08:48 39K all_mrna.sql 2020-09-02 07:33 2.1K xenoMrna.sql 2020-09-02 07:33 2.1K all_mrna.txt.gz 2020-09-02 07:33 2.7M xenoMrna.txt.gz 2020-09-02 07:33 385M mrnaOrientInfo.sql 2020-09-02 07:33 1.8K refFlat.sql 2020-09-02 07:33 1.7K refGene.sql 2020-09-02 07:33 1.9K xenoRefFlat.sql 2020-09-02 07:33 1.7K xenoRefGene.sql 2020-09-02 07:33 1.9K refGene.txt.gz 2020-09-02 07:33 442K refFlat.txt.gz 2020-09-02 07:33 402K xenoRefGene.txt.gz 2020-09-02 07:33 40M xenoRefFlat.txt.gz 2020-09-02 07:33 36M mrnaOrientInfo.txt.gz 2020-09-02 07:33 757K gbLoaded.sql 2020-09-02 07:33 1.6K refSeqAli.sql 2020-09-02 07:33 2.1K xenoRefSeqAli.sql 2020-09-02 07:33 2.1K refSeqAli.txt.gz 2020-09-02 07:33 458K xenoRefSeqAli.txt.gz 2020-09-02 07:33 41M gbLoaded.txt.gz 2020-09-02 07:33 82K 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 netMm39.sql 2020-11-24 20:32 2.1K netMm39.txt.gz 2020-11-24 20:32 58M tableDescriptions.sql 2021-03-13 06:37 1.4K tableDescriptions.txt.gz 2021-03-13 06:37 7.6K trackDb.sql 2021-06-10 16:56 2.1K trackDb.txt.gz 2021-06-10 16:56 55K hgFindSpec.sql 2021-06-10 16:56 1.8K hgFindSpec.txt.gz 2021-06-10 16:56 1.0K tableList.sql 2021-06-13 03:15 1.6K tableList.txt.gz 2021-06-13 03:15 4.0K bigFiles.sql 2021-06-13 03:15 1.4K bigFiles.txt.gz 2021-06-13 03:15 68