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 -
bigFiles.txt.gz 2024-04-28 03:07 87
bigFiles.sql 2024-04-28 03:07 1.4K
tableList.txt.gz 2024-04-28 03:07 6.8K
tableList.sql 2024-04-28 03:07 1.6K
tableDescriptions.txt.gz 2024-04-27 02:04 5.9K
tableDescriptions.sql 2024-04-27 02:04 1.5K
hgFindSpec.txt.gz 2023-03-28 13:53 1.0K
hgFindSpec.sql 2023-03-28 13:53 1.8K
trackDb.txt.gz 2023-03-28 13:53 36K
trackDb.sql 2023-03-28 13:53 2.1K
hgFindSpec_pushedout.txt.gz 2021-12-27 12:23 1.0K
hgFindSpec_pushedout.sql 2021-12-27 12:23 1.8K
trackDb_pushedout.txt.gz 2021-12-27 12:23 36K
trackDb_pushedout.sql 2021-12-27 12:23 2.1K
gbLoaded.txt.gz 2020-09-02 07:33 41K
gbLoaded.sql 2020-09-02 07:33 1.6K
xenoRefSeqAli.txt.gz 2020-09-02 07:33 36M
xenoRefSeqAli.sql 2020-09-02 07:33 2.1K
xenoRefFlat.txt.gz 2020-09-02 07:33 33M
xenoRefFlat.sql 2020-09-02 07:33 1.7K
xenoRefGene.txt.gz 2020-09-02 07:33 37M
xenoRefGene.sql 2020-09-02 07:33 2.0K
mrnaOrientInfo.txt.gz 2020-09-02 07:33 569K
mrnaOrientInfo.sql 2020-09-02 07:33 1.8K
xenoMrna.txt.gz 2020-09-02 07:33 336M
xenoMrna.sql 2020-09-02 07:33 2.1K
all_mrna.txt.gz 2020-09-02 07:33 2.3M
all_mrna.sql 2020-09-02 07:33 2.1K
chr7_mrna.txt.gz 2020-09-02 07:33 245K
chr7_mrna.sql 2020-09-02 07:33 2.1K
chr4_mrna.txt.gz 2020-09-02 07:33 149K
chr4_mrna.sql 2020-09-02 07:33 2.1K
chr1_mrna.txt.gz 2020-09-02 07:33 224K
chr1_mrna.sql 2020-09-02 07:33 2.1K
chr13_mrna.txt.gz 2020-09-02 07:33 122K
chr13_mrna.sql 2020-09-02 07:33 2.1K
chr14_mrna.txt.gz 2020-05-11 17:36 158K
chr14_mrna.sql 2020-05-11 17:36 2.1K
chr8_mrna.txt.gz 2020-05-11 17:36 85K
chr8_mrna.sql 2020-05-11 17:36 2.1K
chr5_mrna.txt.gz 2020-05-11 17:36 132K
chr5_mrna.sql 2020-05-11 17:36 2.1K
chr9_mrna.txt.gz 2020-05-11 17:36 119K
chr9_mrna.sql 2020-05-11 17:36 2.1K
chr17_mrna.txt.gz 2020-05-11 17:36 82K
chr17_mrna.sql 2020-05-11 17:36 2.1K
chr2_mrna.txt.gz 2020-05-11 17:36 197K
chr2_mrna.sql 2020-05-11 17:36 2.1K
chr15_mrna.txt.gz 2020-05-11 17:36 103K
chr15_mrna.sql 2020-05-11 17:36 2.1K
chr12_mrna.txt.gz 2020-05-11 17:36 118K
chr12_mrna.sql 2020-05-11 17:36 2.1K
chr6_mrna.txt.gz 2020-05-11 17:36 168K
chr6_mrna.sql 2020-05-11 17:36 2.1K
chr18_mrna.txt.gz 2020-05-11 17:36 62K
chr18_mrna.sql 2020-05-11 17:36 2.1K
chrX_mrna.txt.gz 2020-05-11 17:36 74K
chrX_mrna.sql 2020-05-11 17:36 2.1K
chr3_mrna.txt.gz 2020-05-11 17:36 141K
chr3_mrna.sql 2020-05-11 17:36 2.1K
chr16_mrna.txt.gz 2020-05-11 17:36 50K
chr16_mrna.sql 2020-05-11 17:36 2.1K
chr11_mrna.txt.gz 2020-05-11 17:13 40K
chr11_mrna.sql 2020-05-11 17:13 2.1K
chr10_mrna.txt.gz 2020-05-11 17:13 60K
chr10_mrna.sql 2020-05-11 17:13 2.1K
chr16_intronEst.txt.gz 2016-07-17 11:28 380K
chr16_intronEst.sql 2016-07-17 11:28 2.1K
chr15_intronEst.txt.gz 2016-07-17 11:28 1.0M
chr15_intronEst.sql 2016-07-17 11:28 2.1K
chr12_intronEst.txt.gz 2016-07-17 11:28 1.3M
chr12_intronEst.sql 2016-07-17 11:28 2.1K
chr10_intronEst.txt.gz 2016-07-17 11:28 529K
chr10_intronEst.sql 2016-07-17 11:28 2.1K
chr11_intronEst.txt.gz 2016-07-17 11:28 379K
chr11_intronEst.sql 2016-07-17 11:28 2.1K
chr2_est.txt.gz 2016-07-17 11:28 4.1M
chr2_est.sql 2016-07-17 11:28 2.1K
chr17_est.txt.gz 2016-07-17 11:28 1.6M
chr17_est.sql 2016-07-17 11:28 2.1K
chr1_intronEst.txt.gz 2016-07-17 11:28 2.7M
chr1_intronEst.sql 2016-07-17 11:28 2.1K
chr14_intronEst.txt.gz 2016-07-17 11:28 1.8M
chr14_intronEst.sql 2016-07-17 11:28 2.1K
all_est.txt.gz 2016-07-17 11:28 50M
all_est.sql 2016-07-17 11:28 2.1K
chr12_est.txt.gz 2016-07-17 11:28 2.3M
chr12_est.sql 2016-07-17 11:28 2.1K
chrM_intronEst.txt.gz 2016-07-17 11:28 495
chrM_intronEst.sql 2016-07-17 11:28 2.1K
chr17_intronEst.txt.gz 2016-07-17 11:28 950K
chr17_intronEst.sql 2016-07-17 11:28 2.1K
chr8_intronEst.txt.gz 2016-07-17 11:28 1.1M
chr8_intronEst.sql 2016-07-17 11:28 2.1K
chr13_intronEst.txt.gz 2016-07-17 11:27 1.2M
chr13_intronEst.sql 2016-07-17 11:27 2.1K
chr10_est.txt.gz 2016-07-17 11:27 1.1M
chr10_est.sql 2016-07-17 11:27 2.1K
chrM_mrna.txt.gz 2016-07-17 11:27 2.9K
chrM_mrna.sql 2016-07-17 11:27 2.1K
chrM_est.txt.gz 2016-07-17 11:27 1.1M
chrM_est.sql 2016-07-17 11:27 2.1K
chr2_intronEst.txt.gz 2016-07-17 11:27 2.3M
chr2_intronEst.sql 2016-07-17 11:27 2.1K
chr14_est.txt.gz 2016-07-17 11:27 3.5M
chr14_est.sql 2016-07-17 11:27 2.1K
chr3_intronEst.txt.gz 2016-07-17 11:27 1.7M
chr3_intronEst.sql 2016-07-17 11:27 2.1K
chr3_est.txt.gz 2016-07-17 11:27 3.2M
chr3_est.sql 2016-07-17 11:27 2.1K
chr18_intronEst.txt.gz 2016-07-17 11:27 466K
chr18_intronEst.sql 2016-07-17 11:27 2.1K
chr4_est.txt.gz 2016-07-17 11:27 3.7M
chr4_est.sql 2016-07-17 11:27 2.1K
chrX_intronEst.txt.gz 2016-07-17 11:27 855K
chrX_intronEst.sql 2016-07-17 11:27 2.1K
chr9_intronEst.txt.gz 2016-07-17 11:27 1.4M
chr9_intronEst.sql 2016-07-17 11:27 2.1K
chr8_est.txt.gz 2016-07-17 11:27 2.0M
chr8_est.sql 2016-07-17 11:27 2.1K
chr9_est.txt.gz 2016-07-17 11:27 2.6M
chr9_est.sql 2016-07-17 11:27 2.1K
estOrientInfo.txt.gz 2016-07-17 11:27 16M
estOrientInfo.sql 2016-07-17 11:27 1.8K
chrX_est.txt.gz 2016-07-17 11:27 1.7M
chrX_est.sql 2016-07-17 11:27 2.1K
chr7_est.txt.gz 2016-07-17 11:27 4.0M
chr7_est.sql 2016-07-17 11:27 2.1K
chr6_intronEst.txt.gz 2016-07-17 11:27 2.0M
chr6_intronEst.sql 2016-07-17 11:27 2.1K
chr16_est.txt.gz 2016-07-17 11:27 936K
chr16_est.sql 2016-07-17 11:27 2.1K
chr6_est.txt.gz 2016-07-17 11:27 3.5M
chr6_est.sql 2016-07-17 11:27 2.1K
chr7_intronEst.txt.gz 2016-07-17 11:27 2.3M
chr7_intronEst.sql 2016-07-17 11:27 2.1K
chr15_est.txt.gz 2016-07-17 11:27 2.2M
chr15_est.sql 2016-07-17 11:27 2.1K
chr13_est.txt.gz 2016-07-17 11:27 2.4M
chr13_est.sql 2016-07-17 11:27 2.1K
chr4_intronEst.txt.gz 2016-07-17 11:27 2.3M
chr4_intronEst.sql 2016-07-17 11:27 2.1K
chr11_est.txt.gz 2016-07-17 11:27 879K
chr11_est.sql 2016-07-17 11:27 2.1K
chr1_est.txt.gz 2016-07-17 11:27 5.2M
chr1_est.sql 2016-07-17 11:27 2.1K
chr5_est.txt.gz 2016-07-17 11:27 3.2M
chr5_est.sql 2016-07-17 11:27 2.1K
chr18_est.txt.gz 2016-07-17 11:25 1.0M
chr18_est.sql 2016-07-17 11:25 2.1K
chr5_intronEst.txt.gz 2016-07-17 11:25 1.7M
chr5_intronEst.sql 2016-07-17 11:25 2.1K
microsat.txt.gz 2015-08-24 02:07 375K
microsat.sql 2015-08-24 02:07 1.5K
augustusGene.txt.gz 2015-07-26 17:28 2.0M
augustusGene.sql 2015-07-26 17:28 1.9K
cpgIslandExtUnmasked.txt.gz 2014-06-01 19:54 1.3M
cpgIslandExtUnmasked.sql 2014-06-01 19:54 1.7K
grp.txt.gz 2014-03-02 04:14 208
grp.sql 2014-03-02 04:14 1.3K
numtSMitochondrion.txt.gz 2013-07-28 06:10 2.8K
numtSMitochondrion.sql 2013-07-28 06:10 1.6K
numtSAssembled.txt.gz 2013-07-28 06:10 2.1K
numtSAssembled.sql 2013-07-28 06:10 1.8K
numtS.txt.gz 2013-07-28 06:10 8.7K
numtS.sql 2013-07-28 06:10 1.7K
bamAllNumtSSorted.txt.gz 2013-07-28 06:10 84
bamAllNumtSSorted.sql 2013-07-28 06:10 1.3K
netBosTau7.txt.gz 2012-06-18 00:04 69M
netBosTau7.sql 2012-06-18 00:03 2.0K
chainBosTau7Link.txt.gz 2012-06-17 23:20 3.1G
chainBosTau7Link.sql 2012-06-17 22:58 1.5K
chainBosTau7.txt.gz 2012-06-17 22:45 786M
chainBosTau7.sql 2012-06-17 22:40 1.6K
tRNAs.txt.gz 2012-04-23 11:59 19K
tRNAs.sql 2012-04-23 11:59 1.7K
ensemblToGeneName.txt.gz 2011-10-04 16:31 118K
ensemblToGeneName.sql 2011-10-04 16:31 1.3K
ensemblSource.txt.gz 2011-10-04 16:31 62K
ensemblSource.sql 2011-10-04 16:31 1.3K
ensGene.txt.gz 2011-10-04 16:28 1.7M
ensGene.sql 2011-10-04 16:28 1.9K
ensGtp.txt.gz 2011-10-04 16:28 167K
ensGtp.sql 2011-10-04 16:28 1.4K
ensPep.txt.gz 2011-10-04 16:28 4.4M
ensPep.sql 2011-10-04 16:28 1.3K
netMonDom5.txt.gz 2010-05-11 17:01 16M
netMonDom5.sql 2010-05-11 17:01 2.0K
chainHg19.txt.gz 2010-05-11 17:01 118M
chainHg19.sql 2010-05-11 17:01 1.6K
blastHg18KG.txt.gz 2010-05-11 17:01 3.7M
blastHg18KG.sql 2010-05-11 17:01 2.1K
chainMm9.txt.gz 2010-05-11 17:00 48M
chainMm9.sql 2010-05-11 17:00 1.6K
chainMonDom5.txt.gz 2010-05-11 16:59 152M
chainMonDom5.sql 2010-05-11 16:59 1.6K
ctgPos2.txt.gz 2010-05-11 16:59 53K
ctgPos2.sql 2010-05-11 16:59 1.5K
nestedRepeats.txt.gz 2010-05-11 16:59 11M
nestedRepeats.sql 2010-05-11 16:59 1.9K
chainMonDom5Link.txt.gz 2010-05-11 16:56 510M
chainMonDom5Link.sql 2010-05-11 16:55 1.5K
gap.txt.gz 2010-05-11 16:55 2.1M
gap.sql 2010-05-11 16:55 1.5K
chainMm9Link.txt.gz 2010-05-11 16:52 419M
chainMm9Link.sql 2010-05-11 16:52 1.5K
gold.txt.gz 2010-05-11 16:52 2.1M
gold.sql 2010-05-11 16:52 1.6K
gc5Base.txt.gz 2010-05-11 16:51 9.4M
gc5Base.sql 2010-05-11 16:51 1.7K
chainHg19Link.txt.gz 2010-05-11 16:48 654M
chainHg19Link.sql 2010-05-11 16:47 1.5K
netMm9.txt.gz 2010-05-11 16:46 51M
netMm9.sql 2010-05-11 16:46 2.0K
netHg19.txt.gz 2010-05-11 16:46 59M
netHg19.sql 2010-05-11 16:46 2.0K
nscanGene.txt.gz 2010-05-11 16:46 1.9M
nscanGene.sql 2010-05-11 16:46 1.9K
history.txt.gz 2010-05-11 16:45 567
history.sql 2010-05-11 16:45 1.5K
rmsk.txt.gz 2010-05-11 16:44 108M
rmsk.sql 2010-05-11 16:44 1.8K
simpleRepeat.txt.gz 2010-05-11 16:44 14M
simpleRepeat.sql 2010-05-11 16:44 1.9K
cpgIslandExt.txt.gz 2010-05-11 16:43 805K
cpgIslandExt.sql 2010-05-11 16:43 1.6K
chromInfo.txt.gz 2010-05-11 16:22 219
chromInfo.sql 2010-05-11 16:22 1.3K