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.
-----------------------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
netMm10.sql 2012-11-16 12:31 2.1K
netMm10.txt.gz 2012-11-16 12:31 58M
gap.sql 2012-11-16 12:32 1.6K
gap.txt.gz 2012-11-16 12:32 1.7M
chainMm10Link.sql 2012-11-16 12:32 1.5K
chainMm10Link.txt.gz 2012-11-16 12:33 509M
simpleRepeat.sql 2012-11-16 12:34 1.9K
simpleRepeat.txt.gz 2012-11-16 12:34 16M
windowmaskerSdust.sql 2012-11-16 12:35 1.5K
windowmaskerSdust.txt.gz 2012-11-16 12:35 126M
chainMm10.sql 2012-11-16 12:35 1.7K
chainMm10.txt.gz 2012-11-16 12:35 63M
cpgIslandExt.sql 2012-11-16 12:35 1.7K
cpgIslandExt.txt.gz 2012-11-16 12:35 917K
rmsk.sql 2012-11-16 12:36 1.9K
rmsk.txt.gz 2012-11-16 12:36 124M
gc5BaseBw.sql 2012-11-16 12:36 1.3K
gc5BaseBw.txt.gz 2012-11-16 12:36 63
genscan.sql 2012-11-16 12:38 1.7K
genscan.txt.gz 2012-11-16 12:38 3.0M
history.sql 2012-11-16 12:38 1.6K
history.txt.gz 2012-11-16 12:38 612
chromInfo.sql 2012-11-16 12:38 1.4K
chromInfo.txt.gz 2012-11-16 12:38 29K
nestedRepeats.sql 2012-11-16 12:39 1.9K
nestedRepeats.txt.gz 2012-11-16 12:39 14M
gold.sql 2012-11-16 12:40 1.7K
gold.txt.gz 2012-11-16 12:40 2.4M
cytoBandIdeo.sql 2013-04-28 22:14 1.5K
cytoBandIdeo.txt.gz 2013-04-28 22:14 26K
ucscToINSDC.sql 2013-09-15 19:49 1.4K
ucscToINSDC.txt.gz 2013-09-15 19:49 37K
pubsBingBlat.sql 2014-01-26 19:12 2.4K
pubsBingBlat.txt.gz 2014-01-26 19:12 1.0M
pubsBingBlatPsl.sql 2014-01-26 19:12 2.2K
pubsBingBlatPsl.txt.gz 2014-01-26 19:12 756K
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
snp138.sql 2014-03-02 04:14 2.9K
snp138.txt.gz 2014-03-02 04:15 369M
snp138CodingDbSnp.sql 2014-03-02 04:17 1.7K
snp138CodingDbSnp.txt.gz 2014-03-02 04:17 3.4M
snp138ExceptionDesc.sql 2014-03-02 04:17 1.4K
snp138ExceptionDesc.txt.gz 2014-03-02 04:17 1.0K
snp138Mult.sql 2014-03-02 04:17 2.9K
snp138Mult.txt.gz 2014-03-02 04:17 1.7M
snp138Seq.sql 2014-03-02 04:17 1.3K
snp138Seq.txt.gz 2014-03-02 04:17 170M
cpgIslandExtUnmasked.sql 2014-06-01 20:00 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 20:00 1.4M
animalQtl.sql 2014-06-30 03:14 1.5K
animalQtl.txt.gz 2014-06-30 03:14 94K
intronEst.sql 2015-04-06 07:30 2.1K
intronEst.txt.gz 2015-04-06 07:30 31M
estOrientInfo.sql 2015-04-06 07:32 1.8K
estOrientInfo.txt.gz 2015-04-06 07:32 18M
all_est.sql 2015-04-06 07:36 2.1K
all_est.txt.gz 2015-04-06 07:36 57M
augustusGene.sql 2015-07-26 17:28 1.9K
augustusGene.txt.gz 2015-07-26 17:28 2.3M
microsat.sql 2015-08-24 02:15 1.5K
microsat.txt.gz 2015-08-24 02:15 399K
ensGtp.sql 2016-11-20 09:45 1.4K
ensGtp.txt.gz 2016-11-20 09:45 283K
ensPep.sql 2016-11-20 09:45 1.3K
ensPep.txt.gz 2016-11-20 09:45 6.5M
ensemblSource.sql 2016-11-20 09:45 1.4K
ensemblSource.txt.gz 2016-11-20 09:45 93K
ensGene.sql 2016-11-20 09:48 1.9K
ensGene.txt.gz 2016-11-20 09:48 2.3M
ensemblToGeneName.sql 2016-11-20 09:48 1.4K
ensemblToGeneName.txt.gz 2016-11-20 09:48 133K
ncbiRefSeq.sql 2018-02-09 13:52 2.0K
ncbiRefSeq.txt.gz 2018-02-09 13:52 3.5M
ncbiRefSeqCurated.sql 2018-02-09 13:52 2.0K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:52 377K
ncbiRefSeqPredicted.sql 2018-02-09 13:52 2.0K
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:52 3.2M
ncbiRefSeqLink.sql 2018-02-09 13:52 2.0K
ncbiRefSeqLink.txt.gz 2018-02-09 13:52 1.8M
ncbiRefSeqPsl.sql 2018-02-09 13:52 2.1K
ncbiRefSeqPsl.txt.gz 2018-02-09 13:52 4.4M
chromAlias.sql 2018-02-18 08:48 1.4K
chromAlias.txt.gz 2018-02-18 08:48 48K
ucscToRefSeq.sql 2018-02-18 08:48 1.4K
ucscToRefSeq.txt.gz 2018-02-18 08:48 39K
extNcbiRefSeq.sql 2018-08-14 02:28 1.5K
extNcbiRefSeq.txt.gz 2018-08-14 02:28 91
ncbiRefSeqCds.sql 2018-08-14 02:28 1.4K
ncbiRefSeqCds.txt.gz 2018-08-14 02:28 325K
ncbiRefSeqOther.sql 2018-08-14 02:28 1.3K
ncbiRefSeqOther.txt.gz 2018-08-14 02:28 75
ncbiRefSeqPepTable.sql 2018-08-14 02:28 1.4K
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:28 9.3M
seqNcbiRefSeq.sql 2018-08-14 02:28 1.6K
seqNcbiRefSeq.txt.gz 2018-08-14 02:28 1.0M
all_mrna.sql 2020-09-02 07:33 2.1K
all_mrna.txt.gz 2020-09-02 07:33 2.7M
xenoMrna.sql 2020-09-02 07:33 2.1K
xenoMrna.txt.gz 2020-09-02 07:33 385M
refGene.sql 2020-09-02 07:33 1.9K
refGene.txt.gz 2020-09-02 07:33 442K
refFlat.sql 2020-09-02 07:33 1.7K
refFlat.txt.gz 2020-09-02 07:33 402K
xenoRefGene.sql 2020-09-02 07:33 2.0K
xenoRefGene.txt.gz 2020-09-02 07:33 40M
xenoRefFlat.sql 2020-09-02 07:33 1.7K
xenoRefFlat.txt.gz 2020-09-02 07:33 36M
mrnaOrientInfo.sql 2020-09-02 07:33 1.8K
mrnaOrientInfo.txt.gz 2020-09-02 07:33 757K
refSeqAli.sql 2020-09-02 07:33 2.1K
refSeqAli.txt.gz 2020-09-02 07:33 458K
xenoRefSeqAli.sql 2020-09-02 07:33 2.1K
xenoRefSeqAli.txt.gz 2020-09-02 07:33 41M
gbLoaded.sql 2020-09-02 07:33 1.6K
gbLoaded.txt.gz 2020-09-02 07:33 82K
chainMm39.sql 2020-11-24 20:26 1.7K
chainMm39.txt.gz 2020-11-24 20:26 53M
chainMm39Link.sql 2020-11-24 20:30 1.6K
chainMm39Link.txt.gz 2020-11-24 20:30 479M
netMm39.sql 2020-11-24 20:32 2.1K
netMm39.txt.gz 2020-11-24 20:32 58M
trackDb.sql 2023-12-05 13:52 2.1K
trackDb.txt.gz 2023-12-05 13:52 53K
trackDb_pushedout.sql 2023-12-05 13:52 2.1K
trackDb_pushedout.txt.gz 2023-12-05 13:52 53K
hgFindSpec.sql 2023-12-05 13:52 1.8K
hgFindSpec.txt.gz 2023-12-05 13:52 1.4K
hgFindSpec_pushedout.sql 2023-12-05 13:52 1.8K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:52 1.5K
tableDescriptions.sql 2024-05-11 02:04 1.5K
tableDescriptions.txt.gz 2024-05-11 02:04 8.5K
tableList.sql 2024-05-12 03:31 1.6K
tableList.txt.gz 2024-05-12 03:31 4.6K
bigFiles.sql 2024-05-12 03:31 1.4K
bigFiles.txt.gz 2024-05-12 03:31 94