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