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 -
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
simpleRepeat.sql 2010-05-11 16:44 1.9K
simpleRepeat.txt.gz 2010-05-11 16:44 14M
rmsk.sql 2010-05-11 16:44 1.8K
rmsk.txt.gz 2010-05-11 16:44 108M
history.sql 2010-05-11 16:45 1.5K
history.txt.gz 2010-05-11 16:45 567
nscanGene.sql 2010-05-11 16:46 1.9K
nscanGene.txt.gz 2010-05-11 16:46 1.9M
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
chainHg19Link.sql 2010-05-11 16:47 1.5K
chainHg19Link.txt.gz 2010-05-11 16:48 654M
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
chainMm9Link.sql 2010-05-11 16:52 1.5K
chainMm9Link.txt.gz 2010-05-11 16:52 419M
gap.sql 2010-05-11 16:55 1.5K
gap.txt.gz 2010-05-11 16:55 2.1M
chainMonDom5Link.sql 2010-05-11 16:55 1.5K
chainMonDom5Link.txt.gz 2010-05-11 16:56 510M
nestedRepeats.sql 2010-05-11 16:59 1.9K
nestedRepeats.txt.gz 2010-05-11 16:59 11M
ctgPos2.sql 2010-05-11 16:59 1.5K
ctgPos2.txt.gz 2010-05-11 16:59 53K
chainMonDom5.sql 2010-05-11 16:59 1.6K
chainMonDom5.txt.gz 2010-05-11 16:59 152M
chainMm9.sql 2010-05-11 17:00 1.6K
chainMm9.txt.gz 2010-05-11 17:00 48M
blastHg18KG.sql 2010-05-11 17:01 2.1K
blastHg18KG.txt.gz 2010-05-11 17:01 3.7M
chainHg19.sql 2010-05-11 17:01 1.6K
chainHg19.txt.gz 2010-05-11 17:01 118M
netMonDom5.sql 2010-05-11 17:01 2.0K
netMonDom5.txt.gz 2010-05-11 17:01 16M
ensPep.sql 2011-10-04 16:28 1.3K
ensPep.txt.gz 2011-10-04 16:28 4.4M
ensGtp.sql 2011-10-04 16:28 1.4K
ensGtp.txt.gz 2011-10-04 16:28 167K
ensGene.sql 2011-10-04 16:28 1.9K
ensGene.txt.gz 2011-10-04 16:28 1.7M
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
tRNAs.sql 2012-04-23 11:59 1.7K
tRNAs.txt.gz 2012-04-23 11:59 19K
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
netBosTau7.sql 2012-06-18 00:03 2.0K
netBosTau7.txt.gz 2012-06-18 00:04 69M
bamAllNumtSSorted.sql 2013-07-28 06:10 1.3K
bamAllNumtSSorted.txt.gz 2013-07-28 06:10 84
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
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 19:54 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 19:54 1.3M
augustusGene.sql 2015-07-26 17:28 1.9K
augustusGene.txt.gz 2015-07-26 17:28 2.0M
microsat.sql 2015-08-24 02:07 1.5K
microsat.txt.gz 2015-08-24 02:07 375K
chr5_intronEst.sql 2016-07-17 11:25 2.1K
chr5_intronEst.txt.gz 2016-07-17 11:25 1.7M
chr18_est.sql 2016-07-17 11:25 2.1K
chr18_est.txt.gz 2016-07-17 11:25 1.0M
chr5_est.sql 2016-07-17 11:27 2.1K
chr5_est.txt.gz 2016-07-17 11:27 3.2M
chr1_est.sql 2016-07-17 11:27 2.1K
chr1_est.txt.gz 2016-07-17 11:27 5.2M
chr11_est.sql 2016-07-17 11:27 2.1K
chr11_est.txt.gz 2016-07-17 11:27 879K
chr4_intronEst.sql 2016-07-17 11:27 2.1K
chr4_intronEst.txt.gz 2016-07-17 11:27 2.3M
chr13_est.sql 2016-07-17 11:27 2.1K
chr13_est.txt.gz 2016-07-17 11:27 2.4M
chr15_est.sql 2016-07-17 11:27 2.1K
chr15_est.txt.gz 2016-07-17 11:27 2.2M
chr7_intronEst.sql 2016-07-17 11:27 2.1K
chr7_intronEst.txt.gz 2016-07-17 11:27 2.3M
chr6_est.sql 2016-07-17 11:27 2.1K
chr6_est.txt.gz 2016-07-17 11:27 3.5M
chr16_est.sql 2016-07-17 11:27 2.1K
chr16_est.txt.gz 2016-07-17 11:27 936K
chr6_intronEst.sql 2016-07-17 11:27 2.1K
chr6_intronEst.txt.gz 2016-07-17 11:27 2.0M
chr7_est.sql 2016-07-17 11:27 2.1K
chr7_est.txt.gz 2016-07-17 11:27 4.0M
chrX_est.sql 2016-07-17 11:27 2.1K
chrX_est.txt.gz 2016-07-17 11:27 1.7M
estOrientInfo.sql 2016-07-17 11:27 1.8K
estOrientInfo.txt.gz 2016-07-17 11:27 16M
chr9_est.sql 2016-07-17 11:27 2.1K
chr9_est.txt.gz 2016-07-17 11:27 2.6M
chr8_est.sql 2016-07-17 11:27 2.1K
chr8_est.txt.gz 2016-07-17 11:27 2.0M
chr9_intronEst.sql 2016-07-17 11:27 2.1K
chr9_intronEst.txt.gz 2016-07-17 11:27 1.4M
chrX_intronEst.sql 2016-07-17 11:27 2.1K
chrX_intronEst.txt.gz 2016-07-17 11:27 855K
chr4_est.sql 2016-07-17 11:27 2.1K
chr4_est.txt.gz 2016-07-17 11:27 3.7M
chr18_intronEst.sql 2016-07-17 11:27 2.1K
chr18_intronEst.txt.gz 2016-07-17 11:27 466K
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
chr14_est.sql 2016-07-17 11:27 2.1K
chr14_est.txt.gz 2016-07-17 11:27 3.5M
chr2_intronEst.sql 2016-07-17 11:27 2.1K
chr2_intronEst.txt.gz 2016-07-17 11:27 2.3M
chrM_est.sql 2016-07-17 11:27 2.1K
chrM_est.txt.gz 2016-07-17 11:27 1.1M
chrM_mrna.sql 2016-07-17 11:27 2.1K
chrM_mrna.txt.gz 2016-07-17 11:27 2.9K
chr10_est.sql 2016-07-17 11:27 2.1K
chr10_est.txt.gz 2016-07-17 11:27 1.1M
chr13_intronEst.sql 2016-07-17 11:27 2.1K
chr13_intronEst.txt.gz 2016-07-17 11:27 1.2M
chr8_intronEst.sql 2016-07-17 11:28 2.1K
chr8_intronEst.txt.gz 2016-07-17 11:28 1.1M
chr17_intronEst.sql 2016-07-17 11:28 2.1K
chr17_intronEst.txt.gz 2016-07-17 11:28 950K
chrM_intronEst.sql 2016-07-17 11:28 2.1K
chrM_intronEst.txt.gz 2016-07-17 11:28 495
chr12_est.sql 2016-07-17 11:28 2.1K
chr12_est.txt.gz 2016-07-17 11:28 2.3M
all_est.sql 2016-07-17 11:28 2.1K
all_est.txt.gz 2016-07-17 11:28 50M
chr14_intronEst.sql 2016-07-17 11:28 2.1K
chr14_intronEst.txt.gz 2016-07-17 11:28 1.8M
chr1_intronEst.sql 2016-07-17 11:28 2.1K
chr1_intronEst.txt.gz 2016-07-17 11:28 2.7M
chr17_est.sql 2016-07-17 11:28 2.1K
chr17_est.txt.gz 2016-07-17 11:28 1.6M
chr2_est.sql 2016-07-17 11:28 2.1K
chr2_est.txt.gz 2016-07-17 11:28 4.1M
chr11_intronEst.sql 2016-07-17 11:28 2.1K
chr11_intronEst.txt.gz 2016-07-17 11:28 379K
chr10_intronEst.sql 2016-07-17 11:28 2.1K
chr10_intronEst.txt.gz 2016-07-17 11:28 529K
chr12_intronEst.sql 2016-07-17 11:28 2.1K
chr12_intronEst.txt.gz 2016-07-17 11:28 1.3M
chr15_intronEst.sql 2016-07-17 11:28 2.1K
chr15_intronEst.txt.gz 2016-07-17 11:28 1.0M
chr16_intronEst.sql 2016-07-17 11:28 2.1K
chr16_intronEst.txt.gz 2016-07-17 11:28 380K
chr10_mrna.sql 2020-05-11 17:13 2.1K
chr10_mrna.txt.gz 2020-05-11 17:13 60K
chr11_mrna.sql 2020-05-11 17:13 2.1K
chr11_mrna.txt.gz 2020-05-11 17:13 40K
chr16_mrna.sql 2020-05-11 17:36 2.1K
chr16_mrna.txt.gz 2020-05-11 17:36 50K
chr3_mrna.sql 2020-05-11 17:36 2.1K
chr3_mrna.txt.gz 2020-05-11 17:36 141K
chrX_mrna.sql 2020-05-11 17:36 2.1K
chrX_mrna.txt.gz 2020-05-11 17:36 74K
chr18_mrna.sql 2020-05-11 17:36 2.1K
chr18_mrna.txt.gz 2020-05-11 17:36 62K
chr6_mrna.sql 2020-05-11 17:36 2.1K
chr6_mrna.txt.gz 2020-05-11 17:36 168K
chr12_mrna.sql 2020-05-11 17:36 2.1K
chr12_mrna.txt.gz 2020-05-11 17:36 118K
chr15_mrna.sql 2020-05-11 17:36 2.1K
chr15_mrna.txt.gz 2020-05-11 17:36 103K
chr2_mrna.sql 2020-05-11 17:36 2.1K
chr2_mrna.txt.gz 2020-05-11 17:36 197K
chr17_mrna.sql 2020-05-11 17:36 2.1K
chr17_mrna.txt.gz 2020-05-11 17:36 82K
chr9_mrna.sql 2020-05-11 17:36 2.1K
chr9_mrna.txt.gz 2020-05-11 17:36 119K
chr5_mrna.sql 2020-05-11 17:36 2.1K
chr5_mrna.txt.gz 2020-05-11 17:36 132K
chr8_mrna.sql 2020-05-11 17:36 2.1K
chr8_mrna.txt.gz 2020-05-11 17:36 85K
chr14_mrna.sql 2020-05-11 17:36 2.1K
chr14_mrna.txt.gz 2020-05-11 17:36 158K
chr13_mrna.sql 2020-09-02 07:33 2.1K
chr13_mrna.txt.gz 2020-09-02 07:33 122K
chr1_mrna.sql 2020-09-02 07:33 2.1K
chr1_mrna.txt.gz 2020-09-02 07:33 224K
chr4_mrna.sql 2020-09-02 07:33 2.1K
chr4_mrna.txt.gz 2020-09-02 07:33 149K
chr7_mrna.sql 2020-09-02 07:33 2.1K
chr7_mrna.txt.gz 2020-09-02 07:33 245K
all_mrna.sql 2020-09-02 07:33 2.1K
all_mrna.txt.gz 2020-09-02 07:33 2.3M
xenoMrna.sql 2020-09-02 07:33 2.1K
xenoMrna.txt.gz 2020-09-02 07:33 336M
mrnaOrientInfo.sql 2020-09-02 07:33 1.8K
mrnaOrientInfo.txt.gz 2020-09-02 07:33 569K
xenoRefGene.sql 2020-09-02 07:33 2.0K
xenoRefGene.txt.gz 2020-09-02 07:33 37M
xenoRefFlat.sql 2020-09-02 07:33 1.7K
xenoRefFlat.txt.gz 2020-09-02 07:33 33M
xenoRefSeqAli.sql 2020-09-02 07:33 2.1K
xenoRefSeqAli.txt.gz 2020-09-02 07:33 36M
gbLoaded.sql 2020-09-02 07:33 1.6K
gbLoaded.txt.gz 2020-09-02 07:33 41K
trackDb_pushedout.sql 2021-12-27 12:23 2.1K
trackDb_pushedout.txt.gz 2021-12-27 12:23 36K
hgFindSpec_pushedout.sql 2021-12-27 12:23 1.8K
hgFindSpec_pushedout.txt.gz 2021-12-27 12:23 1.0K
trackDb.sql 2023-03-28 13:53 2.1K
trackDb.txt.gz 2023-03-28 13:53 36K
hgFindSpec.sql 2023-03-28 13:53 1.8K
hgFindSpec.txt.gz 2023-03-28 13:53 1.0K
tableDescriptions.sql 2024-04-13 02:04 1.5K
tableDescriptions.txt.gz 2024-04-13 02:04 5.9K
tableList.sql 2024-04-14 03:07 1.6K
tableList.txt.gz 2024-04-14 03:07 6.8K
bigFiles.sql 2024-04-14 03:07 1.4K
bigFiles.txt.gz 2024-04-14 03:07 87