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 - bamAllNumtSSorted.txt.gz 2013-07-28 06:10 84 bigFiles.txt.gz 2024-10-13 03:07 87 grp.txt.gz 2014-03-02 04:14 208 chromInfo.txt.gz 2010-05-11 16:22 219 chrM_intronEst.txt.gz 2016-07-17 11:28 495 history.txt.gz 2010-05-11 16:45 567 hgFindSpec.txt.gz 2023-03-28 13:53 1.0K ensPep.sql 2011-10-04 16:28 1.3K ensemblSource.sql 2011-10-04 16:31 1.3K bamAllNumtSSorted.sql 2013-07-28 06:10 1.3K chromInfo.sql 2010-05-11 16:22 1.3K ensemblToGeneName.sql 2011-10-04 16:31 1.3K grp.sql 2014-03-02 04:14 1.3K ensGtp.sql 2011-10-04 16:28 1.4K bigFiles.sql 2024-10-13 03:07 1.4K tableDescriptions.sql 2024-10-12 02:03 1.5K chainMm9Link.sql 2010-05-11 16:52 1.5K chainHg19Link.sql 2010-05-11 16:47 1.5K ctgPos2.sql 2010-05-11 16:59 1.5K chainBosTau7Link.sql 2012-06-17 22:58 1.5K chainMonDom5Link.sql 2010-05-11 16:55 1.5K microsat.sql 2015-08-24 02:07 1.5K history.sql 2010-05-11 16:45 1.5K gap.sql 2010-05-11 16:55 1.5K numtSMitochondrion.sql 2013-07-28 06:10 1.6K tableList.sql 2024-10-13 03:07 1.6K gold.sql 2010-05-11 16:52 1.6K gbLoaded.sql 2020-09-02 07:33 1.6K cpgIslandExt.sql 2010-05-11 16:43 1.6K chainMm9.sql 2010-05-11 17:00 1.6K chainHg19.sql 2010-05-11 17:01 1.6K chainBosTau7.sql 2012-06-17 22:40 1.6K chainMonDom5.sql 2010-05-11 16:59 1.6K tRNAs.sql 2012-04-23 11:59 1.7K gc5Base.sql 2010-05-11 16:51 1.7K cpgIslandExtUnmasked.sql 2014-06-01 19:54 1.7K numtS.sql 2013-07-28 06:10 1.7K xenoRefFlat.sql 2020-09-02 07:33 1.7K hgFindSpec.sql 2023-03-28 13:53 1.8K estOrientInfo.sql 2016-07-17 11:27 1.8K rmsk.sql 2010-05-11 16:44 1.8K mrnaOrientInfo.sql 2020-09-02 07:33 1.8K numtSAssembled.sql 2013-07-28 06:10 1.8K ensGene.sql 2011-10-04 16:28 1.9K nscanGene.sql 2010-05-11 16:46 1.9K simpleRepeat.sql 2010-05-11 16:44 1.9K nestedRepeats.sql 2010-05-11 16:59 1.9K augustusGene.sql 2015-07-26 17:28 1.9K xenoRefGene.sql 2020-09-02 07:33 2.0K netMm9.sql 2010-05-11 16:46 2.0K netHg19.sql 2010-05-11 16:46 2.0K netBosTau7.sql 2012-06-18 00:03 2.0K netMonDom5.sql 2010-05-11 17:01 2.0K blastHg18KG.sql 2010-05-11 17:01 2.1K trackDb.sql 2023-03-28 13:53 2.1K numtSAssembled.txt.gz 2013-07-28 06:10 2.1K chr1_est.sql 2016-07-17 11:27 2.1K chr2_est.sql 2016-07-17 11:28 2.1K chr3_est.sql 2016-07-17 11:27 2.1K chr4_est.sql 2016-07-17 11:27 2.1K chr5_est.sql 2016-07-17 11:27 2.1K chr6_est.sql 2016-07-17 11:27 2.1K chr7_est.sql 2016-07-17 11:27 2.1K chr8_est.sql 2016-07-17 11:27 2.1K chr9_est.sql 2016-07-17 11:27 2.1K chrM_est.sql 2016-07-17 11:27 2.1K chrX_est.sql 2016-07-17 11:27 2.1K chr10_est.sql 2016-07-17 11:27 2.1K chr11_est.sql 2016-07-17 11:27 2.1K chr12_est.sql 2016-07-17 11:28 2.1K chr13_est.sql 2016-07-17 11:27 2.1K chr14_est.sql 2016-07-17 11:27 2.1K chr15_est.sql 2016-07-17 11:27 2.1K chr16_est.sql 2016-07-17 11:27 2.1K chr17_est.sql 2016-07-17 11:28 2.1K chr18_est.sql 2016-07-17 11:25 2.1K chrM_mrna.sql 2016-07-17 11:27 2.1K all_est.sql 2016-07-17 11:28 2.1K chr1_intronEst.sql 2016-07-17 11:28 2.1K chr2_intronEst.sql 2016-07-17 11:27 2.1K chr3_intronEst.sql 2016-07-17 11:27 2.1K chr4_intronEst.sql 2016-07-17 11:27 2.1K chr5_intronEst.sql 2016-07-17 11:25 2.1K chr6_intronEst.sql 2016-07-17 11:27 2.1K chr7_intronEst.sql 2016-07-17 11:27 2.1K chr8_intronEst.sql 2016-07-17 11:28 2.1K chr9_intronEst.sql 2016-07-17 11:27 2.1K chrM_intronEst.sql 2016-07-17 11:28 2.1K chrX_intronEst.sql 2016-07-17 11:27 2.1K chr10_intronEst.sql 2016-07-17 11:28 2.1K chr11_intronEst.sql 2016-07-17 11:28 2.1K chr12_intronEst.sql 2016-07-17 11:28 2.1K chr13_intronEst.sql 2016-07-17 11:27 2.1K chr14_intronEst.sql 2016-07-17 11:28 2.1K chr15_intronEst.sql 2016-07-17 11:28 2.1K chr16_intronEst.sql 2016-07-17 11:28 2.1K chr17_intronEst.sql 2016-07-17 11:28 2.1K chr18_intronEst.sql 2016-07-17 11:27 2.1K chr1_mrna.sql 2020-09-02 07:33 2.1K chr2_mrna.sql 2020-05-11 17:36 2.1K chr3_mrna.sql 2020-05-11 17:36 2.1K chr4_mrna.sql 2020-09-02 07:33 2.1K chr5_mrna.sql 2020-05-11 17:36 2.1K chr6_mrna.sql 2020-05-11 17:36 2.1K chr7_mrna.sql 2020-09-02 07:33 2.1K chr8_mrna.sql 2020-05-11 17:36 2.1K chr9_mrna.sql 2020-05-11 17:36 2.1K chrX_mrna.sql 2020-05-11 17:36 2.1K chr10_mrna.sql 2020-05-11 17:13 2.1K chr11_mrna.sql 2020-05-11 17:13 2.1K chr12_mrna.sql 2020-05-11 17:36 2.1K chr13_mrna.sql 2020-09-02 07:33 2.1K chr14_mrna.sql 2020-05-11 17:36 2.1K chr15_mrna.sql 2020-05-11 17:36 2.1K chr16_mrna.sql 2020-05-11 17:36 2.1K chr17_mrna.sql 2020-05-11 17:36 2.1K chr18_mrna.sql 2020-05-11 17:36 2.1K all_mrna.sql 2020-09-02 07:33 2.1K xenoMrna.sql 2020-09-02 07:33 2.1K xenoRefSeqAli.sql 2020-09-02 07:33 2.1K numtSMitochondrion.txt.gz 2013-07-28 06:10 2.8K chrM_mrna.txt.gz 2016-07-17 11:27 2.9K tableDescriptions.txt.gz 2024-10-12 02:03 5.9K tableList.txt.gz 2024-10-13 03:07 6.7K numtS.txt.gz 2013-07-28 06:10 8.7K tRNAs.txt.gz 2012-04-23 11:59 19K trackDb.txt.gz 2023-03-28 13:53 36K chr11_mrna.txt.gz 2020-05-11 17:13 40K gbLoaded.txt.gz 2020-09-02 07:33 41K chr16_mrna.txt.gz 2020-05-11 17:36 50K ctgPos2.txt.gz 2010-05-11 16:59 53K chr10_mrna.txt.gz 2020-05-11 17:13 60K chr18_mrna.txt.gz 2020-05-11 17:36 62K ensemblSource.txt.gz 2011-10-04 16:31 62K chrX_mrna.txt.gz 2020-05-11 17:36 74K chr17_mrna.txt.gz 2020-05-11 17:36 82K chr8_mrna.txt.gz 2020-05-11 17:36 85K chr15_mrna.txt.gz 2020-05-11 17:36 103K chr12_mrna.txt.gz 2020-05-11 17:36 118K ensemblToGeneName.txt.gz 2011-10-04 16:31 118K chr9_mrna.txt.gz 2020-05-11 17:36 119K chr13_mrna.txt.gz 2020-09-02 07:33 122K chr5_mrna.txt.gz 2020-05-11 17:36 132K chr3_mrna.txt.gz 2020-05-11 17:36 141K chr4_mrna.txt.gz 2020-09-02 07:33 149K chr14_mrna.txt.gz 2020-05-11 17:36 158K ensGtp.txt.gz 2011-10-04 16:28 167K chr6_mrna.txt.gz 2020-05-11 17:36 168K chr2_mrna.txt.gz 2020-05-11 17:36 197K chr1_mrna.txt.gz 2020-09-02 07:33 224K chr7_mrna.txt.gz 2020-09-02 07:33 245K microsat.txt.gz 2015-08-24 02:07 375K chr11_intronEst.txt.gz 2016-07-17 11:28 379K chr16_intronEst.txt.gz 2016-07-17 11:28 380K chr18_intronEst.txt.gz 2016-07-17 11:27 466K chr10_intronEst.txt.gz 2016-07-17 11:28 529K mrnaOrientInfo.txt.gz 2020-09-02 07:33 569K cpgIslandExt.txt.gz 2010-05-11 16:43 805K chrX_intronEst.txt.gz 2016-07-17 11:27 855K chr11_est.txt.gz 2016-07-17 11:27 879K chr16_est.txt.gz 2016-07-17 11:27 936K chr17_intronEst.txt.gz 2016-07-17 11:28 950K chr18_est.txt.gz 2016-07-17 11:25 1.0M chr15_intronEst.txt.gz 2016-07-17 11:28 1.0M chr8_intronEst.txt.gz 2016-07-17 11:28 1.1M chrM_est.txt.gz 2016-07-17 11:27 1.1M chr10_est.txt.gz 2016-07-17 11:27 1.1M chr13_intronEst.txt.gz 2016-07-17 11:27 1.2M cpgIslandExtUnmasked.txt.gz 2014-06-01 19:54 1.3M chr12_intronEst.txt.gz 2016-07-17 11:28 1.3M chr9_intronEst.txt.gz 2016-07-17 11:27 1.4M chr17_est.txt.gz 2016-07-17 11:28 1.6M chrX_est.txt.gz 2016-07-17 11:27 1.7M chr5_intronEst.txt.gz 2016-07-17 11:25 1.7M ensGene.txt.gz 2011-10-04 16:28 1.7M chr3_intronEst.txt.gz 2016-07-17 11:27 1.7M chr14_intronEst.txt.gz 2016-07-17 11:28 1.8M nscanGene.txt.gz 2010-05-11 16:46 1.9M chr8_est.txt.gz 2016-07-17 11:27 2.0M augustusGene.txt.gz 2015-07-26 17:28 2.0M chr6_intronEst.txt.gz 2016-07-17 11:27 2.0M gap.txt.gz 2010-05-11 16:55 2.1M gold.txt.gz 2010-05-11 16:52 2.1M chr15_est.txt.gz 2016-07-17 11:27 2.2M chr12_est.txt.gz 2016-07-17 11:28 2.3M chr4_intronEst.txt.gz 2016-07-17 11:27 2.3M all_mrna.txt.gz 2020-09-02 07:33 2.3M chr2_intronEst.txt.gz 2016-07-17 11:27 2.3M chr7_intronEst.txt.gz 2016-07-17 11:27 2.3M chr13_est.txt.gz 2016-07-17 11:27 2.4M chr9_est.txt.gz 2016-07-17 11:27 2.6M chr1_intronEst.txt.gz 2016-07-17 11:28 2.7M chr5_est.txt.gz 2016-07-17 11:27 3.2M chr3_est.txt.gz 2016-07-17 11:27 3.2M chr14_est.txt.gz 2016-07-17 11:27 3.5M chr6_est.txt.gz 2016-07-17 11:27 3.5M chr4_est.txt.gz 2016-07-17 11:27 3.7M blastHg18KG.txt.gz 2010-05-11 17:01 3.7M chr7_est.txt.gz 2016-07-17 11:27 4.0M chr2_est.txt.gz 2016-07-17 11:28 4.1M ensPep.txt.gz 2011-10-04 16:28 4.4M chr1_est.txt.gz 2016-07-17 11:27 5.2M gc5Base.txt.gz 2010-05-11 16:51 9.4M nestedRepeats.txt.gz 2010-05-11 16:59 11M simpleRepeat.txt.gz 2010-05-11 16:44 14M netMonDom5.txt.gz 2010-05-11 17:01 16M estOrientInfo.txt.gz 2016-07-17 11:27 16M xenoRefFlat.txt.gz 2020-09-02 07:33 33M xenoRefSeqAli.txt.gz 2020-09-02 07:33 36M xenoRefGene.txt.gz 2020-09-02 07:33 37M chainMm9.txt.gz 2010-05-11 17:00 48M all_est.txt.gz 2016-07-17 11:28 50M netMm9.txt.gz 2010-05-11 16:46 51M netHg19.txt.gz 2010-05-11 16:46 59M netBosTau7.txt.gz 2012-06-18 00:04 69M rmsk.txt.gz 2010-05-11 16:44 108M chainHg19.txt.gz 2010-05-11 17:01 118M chainMonDom5.txt.gz 2010-05-11 16:59 152M xenoMrna.txt.gz 2020-09-02 07:33 336M chainMm9Link.txt.gz 2010-05-11 16:52 419M chainMonDom5Link.txt.gz 2010-05-11 16:56 510M chainHg19Link.txt.gz 2010-05-11 16:48 654M chainBosTau7.txt.gz 2012-06-17 22:45 786M chainBosTau7Link.txt.gz 2012-06-17 23:20 3.1G