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 -
xenoRefSeqAli.txt.gz 2020-09-02 07:33 41M
xenoRefSeqAli.sql 2020-09-02 07:33 2.1K
xenoRefGene.txt.gz 2020-09-02 07:33 40M
xenoRefGene.sql 2020-09-02 07:33 2.0K
xenoRefFlat.txt.gz 2020-09-02 07:33 36M
xenoRefFlat.sql 2020-09-02 07:33 1.7K
xenoMrna.txt.gz 2020-09-02 07:33 385M
xenoMrna.sql 2020-09-02 07:33 2.1K
windowmaskerSdust.txt.gz 2012-11-16 12:35 126M
windowmaskerSdust.sql 2012-11-16 12:35 1.5K
ucscToRefSeq.txt.gz 2018-02-18 08:48 39K
ucscToRefSeq.sql 2018-02-18 08:48 1.4K
ucscToINSDC.txt.gz 2013-09-15 19:49 37K
ucscToINSDC.sql 2013-09-15 19:49 1.4K
trackDb.txt.gz 2024-07-25 09:34 85K
trackDb.sql 2024-07-25 09:34 2.1K
tableList.txt.gz 2024-11-24 03:28 4.5K
tableList.sql 2024-11-24 03:28 1.6K
tableDescriptions.txt.gz 2024-11-23 02:03 8.5K
tableDescriptions.sql 2024-11-23 02:03 1.4K
snp138Seq.txt.gz 2014-03-02 04:17 170M
snp138Seq.sql 2014-03-02 04:17 1.3K
snp138Mult.txt.gz 2014-03-02 04:17 1.7M
snp138Mult.sql 2014-03-02 04:17 2.9K
snp138ExceptionDesc.txt.gz 2014-03-02 04:17 1.0K
snp138ExceptionDesc.sql 2014-03-02 04:17 1.4K
snp138CodingDbSnp.txt.gz 2014-03-02 04:17 3.4M
snp138CodingDbSnp.sql 2014-03-02 04:17 1.7K
snp138.txt.gz 2014-03-02 04:15 369M
snp138.sql 2014-03-02 04:14 2.9K
simpleRepeat.txt.gz 2012-11-16 12:34 16M
simpleRepeat.sql 2012-11-16 12:34 1.9K
seqNcbiRefSeq.txt.gz 2018-08-14 02:28 1.0M
seqNcbiRefSeq.sql 2018-08-14 02:28 1.6K
rmsk.txt.gz 2012-11-16 12:36 124M
rmsk.sql 2012-11-16 12:36 1.9K
refSeqAli.txt.gz 2020-09-02 07:33 458K
refSeqAli.sql 2020-09-02 07:33 2.1K
refGene.txt.gz 2020-09-02 07:33 442K
refGene.sql 2020-09-02 07:33 1.9K
refFlat.txt.gz 2020-09-02 07:33 402K
refFlat.sql 2020-09-02 07:33 1.7K
pubsBingBlatPsl.txt.gz 2014-01-26 19:12 756K
pubsBingBlatPsl.sql 2014-01-26 19:12 2.2K
pubsBingBlat.txt.gz 2014-01-26 19:12 1.0M
pubsBingBlat.sql 2014-01-26 19:12 2.4K
netMm39.txt.gz 2020-11-24 20:32 58M
netMm39.sql 2020-11-24 20:32 2.1K
netMm10.txt.gz 2012-11-16 12:31 58M
netMm10.sql 2012-11-16 12:31 2.1K
nestedRepeats.txt.gz 2012-11-16 12:39 14M
nestedRepeats.sql 2012-11-16 12:39 1.9K
ncbiRefSeqPsl.txt.gz 2018-02-09 13:52 4.4M
ncbiRefSeqPsl.sql 2018-02-09 13:52 2.1K
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:52 3.2M
ncbiRefSeqPredicted.sql 2018-02-09 13:52 2.0K
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:28 9.3M
ncbiRefSeqPepTable.sql 2018-08-14 02:28 1.4K
ncbiRefSeqOther.txt.gz 2018-08-14 02:28 75
ncbiRefSeqOther.sql 2018-08-14 02:28 1.3K
ncbiRefSeqLink.txt.gz 2018-02-09 13:52 1.8M
ncbiRefSeqLink.sql 2018-02-09 13:52 2.0K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:52 377K
ncbiRefSeqCurated.sql 2018-02-09 13:52 2.0K
ncbiRefSeqCds.txt.gz 2018-08-14 02:28 325K
ncbiRefSeqCds.sql 2018-08-14 02:28 1.4K
ncbiRefSeq.txt.gz 2018-02-09 13:52 3.5M
ncbiRefSeq.sql 2018-02-09 13:52 2.0K
mrnaOrientInfo.txt.gz 2020-09-02 07:33 757K
mrnaOrientInfo.sql 2020-09-02 07:33 1.8K
microsat.txt.gz 2015-08-24 02:15 399K
microsat.sql 2015-08-24 02:15 1.5K
intronEst.txt.gz 2015-04-06 07:30 31M
intronEst.sql 2015-04-06 07:30 2.1K
history.txt.gz 2012-11-16 12:38 612
history.sql 2012-11-16 12:38 1.6K
hgFindSpec.txt.gz 2024-07-25 09:34 1.5K
hgFindSpec.sql 2024-07-25 09:34 1.8K
grp.txt.gz 2014-03-02 04:14 208
grp.sql 2014-03-02 04:14 1.3K
gold.txt.gz 2012-11-16 12:40 2.4M
gold.sql 2012-11-16 12:40 1.7K
genscan.txt.gz 2012-11-16 12:38 3.0M
genscan.sql 2012-11-16 12:38 1.7K
gc5BaseBw.txt.gz 2012-11-16 12:36 63
gc5BaseBw.sql 2012-11-16 12:36 1.3K
gbLoaded.txt.gz 2020-09-02 07:33 82K
gbLoaded.sql 2020-09-02 07:33 1.6K
gap.txt.gz 2012-11-16 12:32 1.7M
gap.sql 2012-11-16 12:32 1.6K
extNcbiRefSeq.txt.gz 2018-08-14 02:28 91
extNcbiRefSeq.sql 2018-08-14 02:28 1.5K
estOrientInfo.txt.gz 2015-04-06 07:32 18M
estOrientInfo.sql 2015-04-06 07:32 1.8K
ensemblToGeneName.txt.gz 2016-11-20 09:48 133K
ensemblToGeneName.sql 2016-11-20 09:48 1.4K
ensemblSource.txt.gz 2016-11-20 09:45 93K
ensemblSource.sql 2016-11-20 09:45 1.4K
ensPep.txt.gz 2016-11-20 09:45 6.5M
ensPep.sql 2016-11-20 09:45 1.3K
ensGtp.txt.gz 2016-11-20 09:45 283K
ensGtp.sql 2016-11-20 09:45 1.4K
ensGene.txt.gz 2016-11-20 09:48 2.3M
ensGene.sql 2016-11-20 09:48 1.9K
cytoBandIdeo.txt.gz 2013-04-28 22:14 26K
cytoBandIdeo.sql 2013-04-28 22:14 1.5K
cpgIslandExtUnmasked.txt.gz 2014-06-01 20:00 1.4M
cpgIslandExtUnmasked.sql 2014-06-01 20:00 1.7K
cpgIslandExt.txt.gz 2012-11-16 12:35 917K
cpgIslandExt.sql 2012-11-16 12:35 1.7K
chromInfo.txt.gz 2012-11-16 12:38 29K
chromInfo.sql 2012-11-16 12:38 1.4K
chromAlias.txt.gz 2018-02-18 08:48 48K
chromAlias.sql 2018-02-18 08:48 1.4K
chainMm39Link.txt.gz 2020-11-24 20:30 479M
chainMm39Link.sql 2020-11-24 20:30 1.6K
chainMm39.txt.gz 2020-11-24 20:26 53M
chainMm39.sql 2020-11-24 20:26 1.7K
chainMm10Link.txt.gz 2012-11-16 12:33 509M
chainMm10Link.sql 2012-11-16 12:32 1.5K
chainMm10.txt.gz 2012-11-16 12:35 63M
chainMm10.sql 2012-11-16 12:35 1.7K
bigFiles.txt.gz 2024-11-24 03:28 94
bigFiles.sql 2024-11-24 03:28 1.4K
augustusGene.txt.gz 2015-07-26 17:28 2.3M
augustusGene.sql 2015-07-26 17:28 1.9K
animalQtl.txt.gz 2014-06-30 03:14 94K
animalQtl.sql 2014-06-30 03:14 1.5K
all_mrna.txt.gz 2020-09-02 07:33 2.7M
all_mrna.sql 2020-09-02 07:33 2.1K
all_est.txt.gz 2015-04-06 07:36 57M
all_est.sql 2015-04-06 07:36 2.1K