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.
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      Name                        Last modified      Size  Description
Parent Directory - gc5BaseBw.txt.gz 2012-11-16 12:36 63 bigFiles.txt.gz 2021-06-13 03:15 68 grp.txt.gz 2014-03-02 04:14 208 history.txt.gz 2012-11-16 12:38 612 snp138ExceptionDesc.txt.gz 2014-03-02 04:17 1.0K hgFindSpec.txt.gz 2021-06-10 16:56 1.0K gc5BaseBw.sql 2012-11-16 12:36 1.3K ensPep.sql 2016-11-20 09:45 1.3K snp138Seq.sql 2014-03-02 04:17 1.3K grp.sql 2014-03-02 04:14 1.3K ensemblSource.sql 2016-11-20 09:45 1.4K bigFiles.sql 2021-06-13 03:15 1.4K chromInfo.sql 2012-11-16 12:38 1.4K snp138ExceptionDesc.sql 2014-03-02 04:17 1.4K ensemblToGeneName.sql 2016-11-20 09:48 1.4K ensGtp.sql 2016-11-20 09:45 1.4K chromAlias.sql 2018-02-18 08:48 1.4K tableDescriptions.sql 2021-03-13 06:37 1.4K ucscToINSDC.sql 2013-09-15 19:49 1.4K ucscToRefSeq.sql 2018-02-18 08:48 1.4K microsat.sql 2015-08-24 02:15 1.5K animalQtl.sql 2014-06-30 03:14 1.5K windowmaskerSdust.sql 2012-11-16 12:35 1.5K cytoBandIdeo.sql 2013-04-28 22:14 1.5K chainMm10Link.sql 2012-11-16 12:32 1.5K chainMm39Link.sql 2020-11-24 20:30 1.6K tableList.sql 2021-06-13 03:15 1.6K history.sql 2012-11-16 12:38 1.6K gbLoaded.sql 2020-09-02 07:33 1.6K gap.sql 2012-11-16 12:32 1.6K gold.sql 2012-11-16 12:40 1.7K genscan.sql 2012-11-16 12:38 1.7K cpgIslandExt.sql 2012-11-16 12:35 1.7K chainMm10.sql 2012-11-16 12:35 1.7K refFlat.sql 2020-09-02 07:33 1.7K cpgIslandExtUnmasked.sql 2014-06-01 20:00 1.7K xenoRefFlat.sql 2020-09-02 07:33 1.7K chainMm39.sql 2020-11-24 20:26 1.7K snp138CodingDbSnp.sql 2014-03-02 04:17 1.7K hgFindSpec.sql 2021-06-10 16:56 1.8K estOrientInfo.sql 2015-04-06 07:32 1.8K mrnaOrientInfo.sql 2020-09-02 07:33 1.8K rmsk.sql 2012-11-16 12:36 1.9K ensGene.sql 2016-11-20 09:48 1.9K refGene.sql 2020-09-02 07:33 1.9K simpleRepeat.sql 2012-11-16 12:34 1.9K nestedRepeats.sql 2012-11-16 12:39 1.9K xenoRefGene.sql 2020-09-02 07:33 1.9K augustusGene.sql 2015-07-26 17:28 1.9K trackDb.sql 2021-06-10 16:56 2.1K netMm10.sql 2012-11-16 12:31 2.1K all_est.sql 2015-04-06 07:36 2.1K all_mrna.sql 2020-09-02 07:33 2.1K xenoMrna.sql 2020-09-02 07:33 2.1K intronEst.sql 2015-04-06 07:30 2.1K refSeqAli.sql 2020-09-02 07:33 2.1K netMm39.sql 2020-11-24 20:32 2.1K xenoRefSeqAli.sql 2020-09-02 07:33 2.1K pubsBingBlatPsl.sql 2014-01-26 19:12 2.2K pubsBingBlat.sql 2014-01-26 19:12 2.4K snp138.sql 2014-03-02 04:14 2.9K snp138Mult.sql 2014-03-02 04:17 2.9K tableList.txt.gz 2021-06-13 03:15 4.0K tableDescriptions.txt.gz 2021-03-13 06:37 7.6K cytoBandIdeo.txt.gz 2013-04-28 22:14 26K chromInfo.txt.gz 2012-11-16 12:38 29K ucscToINSDC.txt.gz 2013-09-15 19:49 37K ucscToRefSeq.txt.gz 2018-02-18 08:48 39K chromAlias.txt.gz 2018-02-18 08:48 48K trackDb.txt.gz 2021-06-10 16:56 55K gbLoaded.txt.gz 2020-09-02 07:33 82K ensemblSource.txt.gz 2016-11-20 09:45 93K animalQtl.txt.gz 2014-06-30 03:14 94K ensemblToGeneName.txt.gz 2016-11-20 09:48 133K ensGtp.txt.gz 2016-11-20 09:45 283K microsat.txt.gz 2015-08-24 02:15 399K refFlat.txt.gz 2020-09-02 07:33 402K refGene.txt.gz 2020-09-02 07:33 442K refSeqAli.txt.gz 2020-09-02 07:33 458K pubsBingBlatPsl.txt.gz 2014-01-26 19:12 756K mrnaOrientInfo.txt.gz 2020-09-02 07:33 757K cpgIslandExt.txt.gz 2012-11-16 12:35 917K pubsBingBlat.txt.gz 2014-01-26 19:12 1.0M cpgIslandExtUnmasked.txt.gz 2014-06-01 20:00 1.4M snp138Mult.txt.gz 2014-03-02 04:17 1.7M gap.txt.gz 2012-11-16 12:32 1.7M augustusGene.txt.gz 2015-07-26 17:28 2.3M ensGene.txt.gz 2016-11-20 09:48 2.3M gold.txt.gz 2012-11-16 12:40 2.4M all_mrna.txt.gz 2020-09-02 07:33 2.7M genscan.txt.gz 2012-11-16 12:38 3.0M snp138CodingDbSnp.txt.gz 2014-03-02 04:17 3.4M ensPep.txt.gz 2016-11-20 09:45 6.5M nestedRepeats.txt.gz 2012-11-16 12:39 14M simpleRepeat.txt.gz 2012-11-16 12:34 16M estOrientInfo.txt.gz 2015-04-06 07:32 18M intronEst.txt.gz 2015-04-06 07:30 31M xenoRefFlat.txt.gz 2020-09-02 07:33 36M xenoRefGene.txt.gz 2020-09-02 07:33 40M xenoRefSeqAli.txt.gz 2020-09-02 07:33 41M chainMm39.txt.gz 2020-11-24 20:26 53M all_est.txt.gz 2015-04-06 07:36 57M netMm39.txt.gz 2020-11-24 20:32 58M netMm10.txt.gz 2012-11-16 12:31 58M chainMm10.txt.gz 2012-11-16 12:35 63M rmsk.txt.gz 2012-11-16 12:36 124M windowmaskerSdust.txt.gz 2012-11-16 12:35 126M snp138Seq.txt.gz 2014-03-02 04:17 170M snp138.txt.gz 2014-03-02 04:15 369M xenoMrna.txt.gz 2020-09-02 07:33 385M chainMm39Link.txt.gz 2020-11-24 20:30 479M chainMm10Link.txt.gz 2012-11-16 12:33 509M