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.
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Name Last modified Size Description
Parent Directory -
chainMm10Link.txt.gz 2012-11-16 12:33 509M
chainMm39Link.txt.gz 2020-11-24 20:30 479M
xenoMrna.txt.gz 2020-09-02 07:33 385M
snp138.txt.gz 2014-03-02 04:15 369M
snp138Seq.txt.gz 2014-03-02 04:17 170M
windowmaskerSdust.txt.gz 2012-11-16 12:35 126M
rmsk.txt.gz 2012-11-16 12:36 124M
chainMm10.txt.gz 2012-11-16 12:35 63M
netMm10.txt.gz 2012-11-16 12:31 58M
netMm39.txt.gz 2020-11-24 20:32 58M
all_est.txt.gz 2015-04-06 07:36 57M
chainMm39.txt.gz 2020-11-24 20:26 53M
xenoRefSeqAli.txt.gz 2020-09-02 07:33 41M
xenoRefGene.txt.gz 2020-09-02 07:33 40M
xenoRefFlat.txt.gz 2020-09-02 07:33 36M
intronEst.txt.gz 2015-04-06 07:30 31M
estOrientInfo.txt.gz 2015-04-06 07:32 18M
simpleRepeat.txt.gz 2012-11-16 12:34 16M
nestedRepeats.txt.gz 2012-11-16 12:39 14M
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:28 9.3M
ensPep.txt.gz 2016-11-20 09:45 6.5M
ncbiRefSeqPsl.txt.gz 2018-02-09 13:52 4.4M
ncbiRefSeq.txt.gz 2018-02-09 13:52 3.5M
snp138CodingDbSnp.txt.gz 2014-03-02 04:17 3.4M
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:52 3.2M
genscan.txt.gz 2012-11-16 12:38 3.0M
all_mrna.txt.gz 2020-09-02 07:33 2.7M
gold.txt.gz 2012-11-16 12:40 2.4M
ensGene.txt.gz 2016-11-20 09:48 2.3M
augustusGene.txt.gz 2015-07-26 17:28 2.3M
ncbiRefSeqLink.txt.gz 2018-02-09 13:52 1.8M
gap.txt.gz 2012-11-16 12:32 1.7M
snp138Mult.txt.gz 2014-03-02 04:17 1.7M
cpgIslandExtUnmasked.txt.gz 2014-06-01 20:00 1.4M
pubsBingBlat.txt.gz 2014-01-26 19:12 1.0M
seqNcbiRefSeq.txt.gz 2018-08-14 02:28 1.0M
cpgIslandExt.txt.gz 2012-11-16 12:35 917K
mrnaOrientInfo.txt.gz 2020-09-02 07:33 757K
pubsBingBlatPsl.txt.gz 2014-01-26 19:12 756K
refSeqAli.txt.gz 2020-09-02 07:33 458K
refGene.txt.gz 2020-09-02 07:33 442K
refFlat.txt.gz 2020-09-02 07:33 402K
microsat.txt.gz 2015-08-24 02:15 399K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:52 377K
ncbiRefSeqCds.txt.gz 2018-08-14 02:28 325K
ensGtp.txt.gz 2016-11-20 09:45 283K
ensemblToGeneName.txt.gz 2016-11-20 09:48 133K
animalQtl.txt.gz 2014-06-30 03:14 94K
ensemblSource.txt.gz 2016-11-20 09:45 93K
trackDb.txt.gz 2024-07-25 09:34 85K
gbLoaded.txt.gz 2020-09-02 07:33 82K
chromAlias.txt.gz 2018-02-18 08:48 48K
ucscToRefSeq.txt.gz 2018-02-18 08:48 39K
ucscToINSDC.txt.gz 2013-09-15 19:49 37K
chromInfo.txt.gz 2012-11-16 12:38 29K
cytoBandIdeo.txt.gz 2013-04-28 22:14 26K
tableDescriptions.txt.gz 2024-11-16 02:03 8.5K
tableList.txt.gz 2024-11-17 03:41 4.5K
snp138Mult.sql 2014-03-02 04:17 2.9K
snp138.sql 2014-03-02 04:14 2.9K
pubsBingBlat.sql 2014-01-26 19:12 2.4K
pubsBingBlatPsl.sql 2014-01-26 19:12 2.2K
xenoRefSeqAli.sql 2020-09-02 07:33 2.1K
ncbiRefSeqPsl.sql 2018-02-09 13:52 2.1K
refSeqAli.sql 2020-09-02 07:33 2.1K
xenoMrna.sql 2020-09-02 07:33 2.1K
all_mrna.sql 2020-09-02 07:33 2.1K
netMm39.sql 2020-11-24 20:32 2.1K
intronEst.sql 2015-04-06 07:30 2.1K
all_est.sql 2015-04-06 07:36 2.1K
netMm10.sql 2012-11-16 12:31 2.1K
trackDb.sql 2024-07-25 09:34 2.1K
ncbiRefSeqLink.sql 2018-02-09 13:52 2.0K
ncbiRefSeqPredicted.sql 2018-02-09 13:52 2.0K
ncbiRefSeqCurated.sql 2018-02-09 13:52 2.0K
xenoRefGene.sql 2020-09-02 07:33 2.0K
ncbiRefSeq.sql 2018-02-09 13:52 2.0K
refGene.sql 2020-09-02 07:33 1.9K
augustusGene.sql 2015-07-26 17:28 1.9K
nestedRepeats.sql 2012-11-16 12:39 1.9K
simpleRepeat.sql 2012-11-16 12:34 1.9K
ensGene.sql 2016-11-20 09:48 1.9K
rmsk.sql 2012-11-16 12:36 1.9K
mrnaOrientInfo.sql 2020-09-02 07:33 1.8K
hgFindSpec.sql 2024-07-25 09:34 1.8K
estOrientInfo.sql 2015-04-06 07:32 1.8K
xenoRefFlat.sql 2020-09-02 07:33 1.7K
snp138CodingDbSnp.sql 2014-03-02 04:17 1.7K
refFlat.sql 2020-09-02 07:33 1.7K
chainMm39.sql 2020-11-24 20:26 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 20:00 1.7K
chainMm10.sql 2012-11-16 12:35 1.7K
cpgIslandExt.sql 2012-11-16 12:35 1.7K
genscan.sql 2012-11-16 12:38 1.7K
gold.sql 2012-11-16 12:40 1.7K
gbLoaded.sql 2020-09-02 07:33 1.6K
gap.sql 2012-11-16 12:32 1.6K
tableList.sql 2024-11-17 03:41 1.6K
history.sql 2012-11-16 12:38 1.6K
seqNcbiRefSeq.sql 2018-08-14 02:28 1.6K
chainMm39Link.sql 2020-11-24 20:30 1.6K
chainMm10Link.sql 2012-11-16 12:32 1.5K
cytoBandIdeo.sql 2013-04-28 22:14 1.5K
windowmaskerSdust.sql 2012-11-16 12:35 1.5K
animalQtl.sql 2014-06-30 03:14 1.5K
microsat.sql 2015-08-24 02:15 1.5K
hgFindSpec.txt.gz 2024-07-25 09:34 1.5K
extNcbiRefSeq.sql 2018-08-14 02:28 1.5K
tableDescriptions.sql 2024-11-16 02:03 1.5K
ucscToRefSeq.sql 2018-02-18 08:48 1.4K
ucscToINSDC.sql 2013-09-15 19:49 1.4K
chromAlias.sql 2018-02-18 08:48 1.4K
ensGtp.sql 2016-11-20 09:45 1.4K
bigFiles.sql 2024-11-17 03:41 1.4K
ensemblToGeneName.sql 2016-11-20 09:48 1.4K
snp138ExceptionDesc.sql 2014-03-02 04:17 1.4K
chromInfo.sql 2012-11-16 12:38 1.4K
ncbiRefSeqPepTable.sql 2018-08-14 02:28 1.4K
ncbiRefSeqCds.sql 2018-08-14 02:28 1.4K
ensemblSource.sql 2016-11-20 09:45 1.4K
grp.sql 2014-03-02 04:14 1.3K
snp138Seq.sql 2014-03-02 04:17 1.3K
ensPep.sql 2016-11-20 09:45 1.3K
ncbiRefSeqOther.sql 2018-08-14 02:28 1.3K
gc5BaseBw.sql 2012-11-16 12:36 1.3K
snp138ExceptionDesc.txt.gz 2014-03-02 04:17 1.0K
history.txt.gz 2012-11-16 12:38 612
grp.txt.gz 2014-03-02 04:14 208
bigFiles.txt.gz 2024-11-17 03:41 94
extNcbiRefSeq.txt.gz 2018-08-14 02:28 91
ncbiRefSeqOther.txt.gz 2018-08-14 02:28 75
gc5BaseBw.txt.gz 2012-11-16 12:36 63