This directory contains a dump of the UCSC genome annotation database for
Nov. 2009 (SGSC Sscrofa9.2/susScr2) assembly of the pig
genome (susScr2, SGSC Sscrofa9.2 (NCBI project 10718, GCA_000003025.2)),
The annotations were generated by UCSC and collaborators worldwide.

This assembly was produced by the Swine Genome Sequencing Consortium
and Wellcome Trust Sange Institute.

For more information on the pig genome, see the project website:
http://piggenome.org/
http://www.sanger.ac.uk/resources/


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=susScr2
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/susScr2/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/susScr2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/susScr2/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr2/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr2/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 susScr2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql susScr2 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

All the files and tables in this directory are freely usable for any purpose.
      Name                        Last modified      Size  Description
Parent Directory - all_est.sql 2016-07-17 11:28 2.1K all_est.txt.gz 2016-07-17 11:28 50M all_mrna.sql 2020-09-02 07:33 2.1K all_mrna.txt.gz 2020-09-02 07:33 2.3M augustusGene.sql 2015-07-26 17:28 1.9K augustusGene.txt.gz 2015-07-26 17:28 2.0M bamAllNumtSSorted.sql 2013-07-28 06:10 1.3K bamAllNumtSSorted.txt.gz 2013-07-28 06:10 84 bigFiles.sql 2021-05-09 03:03 1.4K bigFiles.txt.gz 2021-05-09 03:03 87 blastHg18KG.sql 2010-05-11 17:01 2.1K blastHg18KG.txt.gz 2010-05-11 17:01 3.7M chainBosTau7.sql 2012-06-17 22:40 1.6K chainBosTau7.txt.gz 2012-06-17 22:45 786M chainBosTau7Link.sql 2012-06-17 22:58 1.5K chainBosTau7Link.txt.gz 2012-06-17 23:20 3.1G chainHg19.sql 2010-05-11 17:01 1.6K chainHg19.txt.gz 2010-05-11 17:01 118M chainHg19Link.sql 2010-05-11 16:47 1.5K chainHg19Link.txt.gz 2010-05-11 16:48 654M chainMm9.sql 2010-05-11 17:00 1.6K chainMm9.txt.gz 2010-05-11 17:00 48M chainMm9Link.sql 2010-05-11 16:52 1.5K chainMm9Link.txt.gz 2010-05-11 16:52 419M chainMonDom5.sql 2010-05-11 16:59 1.6K chainMonDom5.txt.gz 2010-05-11 16:59 152M chainMonDom5Link.sql 2010-05-11 16:55 1.5K chainMonDom5Link.txt.gz 2010-05-11 16:56 510M chr1_est.sql 2016-07-17 11:27 2.1K chr1_est.txt.gz 2016-07-17 11:27 5.2M chr1_intronEst.sql 2016-07-17 11:28 2.1K chr1_intronEst.txt.gz 2016-07-17 11:28 2.7M chr1_mrna.sql 2020-09-02 07:33 2.1K chr1_mrna.txt.gz 2020-09-02 07:33 224K chr2_est.sql 2016-07-17 11:28 2.1K chr2_est.txt.gz 2016-07-17 11:28 4.1M chr2_intronEst.sql 2016-07-17 11:27 2.1K chr2_intronEst.txt.gz 2016-07-17 11:27 2.3M chr2_mrna.sql 2020-05-11 17:36 2.1K chr2_mrna.txt.gz 2020-05-11 17:36 197K chr3_est.sql 2016-07-17 11:27 2.1K chr3_est.txt.gz 2016-07-17 11:27 3.2M chr3_intronEst.sql 2016-07-17 11:27 2.1K chr3_intronEst.txt.gz 2016-07-17 11:27 1.7M chr3_mrna.sql 2020-05-11 17:36 2.1K chr3_mrna.txt.gz 2020-05-11 17:36 141K chr4_est.sql 2016-07-17 11:27 2.1K chr4_est.txt.gz 2016-07-17 11:27 3.7M chr4_intronEst.sql 2016-07-17 11:27 2.1K chr4_intronEst.txt.gz 2016-07-17 11:27 2.3M chr4_mrna.sql 2020-09-02 07:33 2.1K chr4_mrna.txt.gz 2020-09-02 07:33 149K chr5_est.sql 2016-07-17 11:27 2.1K chr5_est.txt.gz 2016-07-17 11:27 3.2M chr5_intronEst.sql 2016-07-17 11:25 2.1K chr5_intronEst.txt.gz 2016-07-17 11:25 1.7M chr5_mrna.sql 2020-05-11 17:36 2.1K chr5_mrna.txt.gz 2020-05-11 17:36 132K chr6_est.sql 2016-07-17 11:27 2.1K chr6_est.txt.gz 2016-07-17 11:27 3.5M chr6_intronEst.sql 2016-07-17 11:27 2.1K chr6_intronEst.txt.gz 2016-07-17 11:27 2.0M chr6_mrna.sql 2020-05-11 17:36 2.1K chr6_mrna.txt.gz 2020-05-11 17:36 168K chr7_est.sql 2016-07-17 11:27 2.1K chr7_est.txt.gz 2016-07-17 11:27 4.0M chr7_intronEst.sql 2016-07-17 11:27 2.1K chr7_intronEst.txt.gz 2016-07-17 11:27 2.3M chr7_mrna.sql 2020-09-02 07:33 2.1K chr7_mrna.txt.gz 2020-09-02 07:33 245K chr8_est.sql 2016-07-17 11:27 2.1K chr8_est.txt.gz 2016-07-17 11:27 2.0M chr8_intronEst.sql 2016-07-17 11:28 2.1K chr8_intronEst.txt.gz 2016-07-17 11:28 1.1M chr8_mrna.sql 2020-05-11 17:36 2.1K chr8_mrna.txt.gz 2020-05-11 17:36 85K chr9_est.sql 2016-07-17 11:27 2.1K chr9_est.txt.gz 2016-07-17 11:27 2.6M chr9_intronEst.sql 2016-07-17 11:27 2.1K chr9_intronEst.txt.gz 2016-07-17 11:27 1.4M chr9_mrna.sql 2020-05-11 17:36 2.1K chr9_mrna.txt.gz 2020-05-11 17:36 119K chr10_est.sql 2016-07-17 11:27 2.1K chr10_est.txt.gz 2016-07-17 11:27 1.1M chr10_intronEst.sql 2016-07-17 11:28 2.1K chr10_intronEst.txt.gz 2016-07-17 11:28 529K chr10_mrna.sql 2020-05-11 17:13 2.1K chr10_mrna.txt.gz 2020-05-11 17:13 60K chr11_est.sql 2016-07-17 11:27 2.1K chr11_est.txt.gz 2016-07-17 11:27 879K chr11_intronEst.sql 2016-07-17 11:28 2.1K chr11_intronEst.txt.gz 2016-07-17 11:28 379K chr11_mrna.sql 2020-05-11 17:13 2.1K chr11_mrna.txt.gz 2020-05-11 17:13 40K chr12_est.sql 2016-07-17 11:28 2.1K chr12_est.txt.gz 2016-07-17 11:28 2.3M chr12_intronEst.sql 2016-07-17 11:28 2.1K chr12_intronEst.txt.gz 2016-07-17 11:28 1.3M chr12_mrna.sql 2020-05-11 17:36 2.1K chr12_mrna.txt.gz 2020-05-11 17:36 118K chr13_est.sql 2016-07-17 11:27 2.1K chr13_est.txt.gz 2016-07-17 11:27 2.4M chr13_intronEst.sql 2016-07-17 11:27 2.1K chr13_intronEst.txt.gz 2016-07-17 11:27 1.2M chr13_mrna.sql 2020-09-02 07:33 2.1K chr13_mrna.txt.gz 2020-09-02 07:33 122K chr14_est.sql 2016-07-17 11:27 2.1K chr14_est.txt.gz 2016-07-17 11:27 3.5M chr14_intronEst.sql 2016-07-17 11:28 2.1K chr14_intronEst.txt.gz 2016-07-17 11:28 1.8M chr14_mrna.sql 2020-05-11 17:36 2.1K chr14_mrna.txt.gz 2020-05-11 17:36 158K chr15_est.sql 2016-07-17 11:27 2.1K chr15_est.txt.gz 2016-07-17 11:27 2.2M chr15_intronEst.sql 2016-07-17 11:28 2.1K chr15_intronEst.txt.gz 2016-07-17 11:28 1.0M chr15_mrna.sql 2020-05-11 17:36 2.1K chr15_mrna.txt.gz 2020-05-11 17:36 103K chr16_est.sql 2016-07-17 11:27 2.1K chr16_est.txt.gz 2016-07-17 11:27 936K chr16_intronEst.sql 2016-07-17 11:28 2.1K chr16_intronEst.txt.gz 2016-07-17 11:28 380K chr16_mrna.sql 2020-05-11 17:36 2.1K chr16_mrna.txt.gz 2020-05-11 17:36 50K chr17_est.sql 2016-07-17 11:28 2.1K chr17_est.txt.gz 2016-07-17 11:28 1.6M chr17_intronEst.sql 2016-07-17 11:28 2.1K chr17_intronEst.txt.gz 2016-07-17 11:28 950K chr17_mrna.sql 2020-05-11 17:36 2.1K chr17_mrna.txt.gz 2020-05-11 17:36 82K chr18_est.sql 2016-07-17 11:25 2.1K chr18_est.txt.gz 2016-07-17 11:25 1.0M chr18_intronEst.sql 2016-07-17 11:27 2.1K chr18_intronEst.txt.gz 2016-07-17 11:27 466K chr18_mrna.sql 2020-05-11 17:36 2.1K chr18_mrna.txt.gz 2020-05-11 17:36 62K chrM_est.sql 2016-07-17 11:27 2.1K chrM_est.txt.gz 2016-07-17 11:27 1.1M chrM_intronEst.sql 2016-07-17 11:28 2.1K chrM_intronEst.txt.gz 2016-07-17 11:28 495 chrM_mrna.sql 2016-07-17 11:27 2.1K chrM_mrna.txt.gz 2016-07-17 11:27 2.9K chrX_est.sql 2016-07-17 11:27 2.1K chrX_est.txt.gz 2016-07-17 11:27 1.7M chrX_intronEst.sql 2016-07-17 11:27 2.1K chrX_intronEst.txt.gz 2016-07-17 11:27 855K chrX_mrna.sql 2020-05-11 17:36 2.1K chrX_mrna.txt.gz 2020-05-11 17:36 74K chromInfo.sql 2010-05-11 16:22 1.3K chromInfo.txt.gz 2010-05-11 16:22 219 cpgIslandExt.sql 2010-05-11 16:43 1.6K cpgIslandExt.txt.gz 2010-05-11 16:43 805K cpgIslandExtUnmasked.sql 2014-06-01 19:54 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 19:54 1.3M ctgPos2.sql 2010-05-11 16:59 1.5K ctgPos2.txt.gz 2010-05-11 16:59 53K ensGene.sql 2011-10-04 16:28 1.9K ensGene.txt.gz 2011-10-04 16:28 1.7M ensGtp.sql 2011-10-04 16:28 1.4K ensGtp.txt.gz 2011-10-04 16:28 167K ensPep.sql 2011-10-04 16:28 1.3K ensPep.txt.gz 2011-10-04 16:28 4.4M ensemblSource.sql 2011-10-04 16:31 1.3K ensemblSource.txt.gz 2011-10-04 16:31 62K ensemblToGeneName.sql 2011-10-04 16:31 1.3K ensemblToGeneName.txt.gz 2011-10-04 16:31 118K estOrientInfo.sql 2016-07-17 11:27 1.8K estOrientInfo.txt.gz 2016-07-17 11:27 16M gap.sql 2010-05-11 16:55 1.5K gap.txt.gz 2010-05-11 16:55 2.1M gbLoaded.sql 2020-09-02 07:33 1.6K gbLoaded.txt.gz 2020-09-02 07:33 41K gc5Base.sql 2010-05-11 16:51 1.7K gc5Base.txt.gz 2010-05-11 16:51 9.4M gold.sql 2010-05-11 16:52 1.6K gold.txt.gz 2010-05-11 16:52 2.1M grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.sql 2020-10-25 08:29 1.7K hgFindSpec.txt.gz 2020-10-25 08:29 963 history.sql 2010-05-11 16:45 1.5K history.txt.gz 2010-05-11 16:45 567 microsat.sql 2015-08-24 02:07 1.5K microsat.txt.gz 2015-08-24 02:07 375K mrnaOrientInfo.sql 2020-09-02 07:33 1.8K mrnaOrientInfo.txt.gz 2020-09-02 07:33 569K nestedRepeats.sql 2010-05-11 16:59 1.9K nestedRepeats.txt.gz 2010-05-11 16:59 11M netBosTau7.sql 2012-06-18 00:03 2.0K netBosTau7.txt.gz 2012-06-18 00:04 69M netHg19.sql 2010-05-11 16:46 2.0K netHg19.txt.gz 2010-05-11 16:46 59M netMm9.sql 2010-05-11 16:46 2.0K netMm9.txt.gz 2010-05-11 16:46 51M netMonDom5.sql 2010-05-11 17:01 2.0K netMonDom5.txt.gz 2010-05-11 17:01 16M nscanGene.sql 2010-05-11 16:46 1.9K nscanGene.txt.gz 2010-05-11 16:46 1.9M numtS.sql 2013-07-28 06:10 1.7K numtS.txt.gz 2013-07-28 06:10 8.7K numtSAssembled.sql 2013-07-28 06:10 1.8K numtSAssembled.txt.gz 2013-07-28 06:10 2.1K numtSMitochondrion.sql 2013-07-28 06:10 1.6K numtSMitochondrion.txt.gz 2013-07-28 06:10 2.8K rmsk.sql 2010-05-11 16:44 1.8K rmsk.txt.gz 2010-05-11 16:44 108M simpleRepeat.sql 2010-05-11 16:44 1.9K simpleRepeat.txt.gz 2010-05-11 16:44 14M tRNAs.sql 2012-04-23 11:59 1.7K tRNAs.txt.gz 2012-04-23 11:59 19K tableDescriptions.sql 2021-01-14 06:34 1.4K tableDescriptions.txt.gz 2021-01-14 06:34 5.8K tableList.sql 2021-05-09 03:03 1.6K tableList.txt.gz 2021-05-09 03:03 6.7K trackDb.sql 2020-10-25 08:29 2.0K trackDb.txt.gz 2020-10-25 08:29 35K xenoMrna.sql 2020-09-02 07:33 2.1K xenoMrna.txt.gz 2020-09-02 07:33 336M xenoRefFlat.sql 2020-09-02 07:33 1.7K xenoRefFlat.txt.gz 2020-09-02 07:33 33M xenoRefGene.sql 2020-09-02 07:33 1.9K xenoRefGene.txt.gz 2020-09-02 07:33 37M xenoRefSeqAli.sql 2020-09-02 07:33 2.1K xenoRefSeqAli.txt.gz 2020-09-02 07:33 36M