This directory contains a dump of the UCSC genome annotation database for the
Aug. 2012 (ISGC Oar_v3.1/oviAri3) assembly of the sheep genome
(oviAri3, International Sheep Genome Consortium) .
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/83
http://www.ncbi.nlm.nih.gov/genome/assembly/457978
http://www.ncbi.nlm.nih.gov/bioproject/179263
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=oviAri3
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/oviAri3/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/oviAri3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/oviAri3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/oviAri3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/oviAri3/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 oviAri3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql oviAri3 --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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
chainHg19Link.sql 2013-08-30 12:21 1.5K
chainHg19Link.txt.gz 2013-08-30 12:22 816M
chromInfo.sql 2013-08-30 12:31 1.4K
chromInfo.txt.gz 2013-08-30 12:31 34K
genscan.sql 2013-08-30 12:31 1.7K
genscan.txt.gz 2013-08-30 12:31 3.0M
history.sql 2013-08-30 12:31 1.6K
history.txt.gz 2013-08-30 12:31 392
netHg19.sql 2013-08-30 12:31 2.1K
netHg19.txt.gz 2013-08-30 12:31 66M
gap.sql 2013-08-30 12:31 1.6K
gap.txt.gz 2013-08-30 12:31 1.7M
rmsk.sql 2013-08-30 12:31 1.9K
rmsk.txt.gz 2013-08-30 12:32 135M
genscanSubopt.sql 2013-08-30 12:32 1.6K
genscanSubopt.txt.gz 2013-08-30 12:32 5.8M
cpgIslandExt.sql 2013-08-30 12:32 1.7K
cpgIslandExt.txt.gz 2013-08-30 12:32 810K
gold.sql 2013-08-30 12:32 1.7K
gold.txt.gz 2013-08-30 12:32 2.3M
simpleRepeat.sql 2013-08-30 12:32 1.9K
simpleRepeat.txt.gz 2013-08-30 12:32 17M
nestedRepeats.sql 2013-08-30 12:32 1.9K
nestedRepeats.txt.gz 2013-08-30 12:32 14M
chainHg19.sql 2013-08-30 12:33 1.7K
chainHg19.txt.gz 2013-08-30 12:33 189M
gc5BaseBw.sql 2013-08-30 12:33 1.3K
gc5BaseBw.txt.gz 2013-08-30 12:33 63
windowmaskerSdust.sql 2013-08-30 12:33 1.5K
windowmaskerSdust.txt.gz 2013-08-30 12:34 121M
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 18:04 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 18:04 918K
animalQtl.sql 2014-06-30 01:24 1.5K
animalQtl.txt.gz 2014-06-30 01:24 8.9K
cytoBandIdeo.sql 2014-12-14 19:18 1.5K
cytoBandIdeo.txt.gz 2014-12-14 19:18 32K
augustusGene.sql 2015-07-26 17:21 1.9K
augustusGene.txt.gz 2015-07-26 17:21 2.2M
microsat.sql 2015-08-23 23:18 1.5K
microsat.txt.gz 2015-08-23 23:18 301K
all_est.sql 2016-05-15 11:01 2.1K
all_est.txt.gz 2016-05-15 11:01 13M
estOrientInfo.sql 2016-05-15 11:01 1.8K
estOrientInfo.txt.gz 2016-05-15 11:01 3.8M
intronEst.sql 2016-05-15 11:02 2.1K
intronEst.txt.gz 2016-05-15 11:02 8.1M
ncbiRefSeq.sql 2018-02-09 13:49 2.0K
ncbiRefSeq.txt.gz 2018-02-09 13:49 3.3M
ncbiRefSeqCurated.sql 2018-02-09 13:49 2.0K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:49 70K
ncbiRefSeqPredicted.sql 2018-02-09 13:49 2.0K
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:49 3.2M
ncbiRefSeqLink.sql 2018-02-09 13:49 2.0K
ncbiRefSeqLink.txt.gz 2018-02-09 13:49 1.6M
ncbiRefSeqPsl.sql 2018-02-09 13:49 2.1K
ncbiRefSeqPsl.txt.gz 2018-02-09 13:49 4.4M
chromAlias.sql 2018-02-18 07:59 1.4K
chromAlias.txt.gz 2018-02-18 07:59 61K
ucscToRefSeq.sql 2018-02-18 07:59 1.4K
ucscToRefSeq.txt.gz 2018-02-18 07:59 47K
extNcbiRefSeq.sql 2018-08-14 02:29 1.5K
extNcbiRefSeq.txt.gz 2018-08-14 02:29 91
ncbiRefSeqCds.sql 2018-08-14 02:29 1.4K
ncbiRefSeqCds.txt.gz 2018-08-14 02:29 331K
ncbiRefSeqOther.sql 2018-08-14 02:29 1.3K
ncbiRefSeqOther.txt.gz 2018-08-14 02:29 75
ncbiRefSeqPepTable.sql 2018-08-14 02:29 1.4K
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:29 8.5M
seqNcbiRefSeq.sql 2018-08-14 02:29 1.6K
seqNcbiRefSeq.txt.gz 2018-08-14 02:29 948K
all_mrna.sql 2020-08-22 15:54 2.1K
all_mrna.txt.gz 2020-08-22 15:54 215K
xenoMrna.sql 2020-08-22 15:54 2.1K
xenoMrna.txt.gz 2020-08-22 15:54 223M
refGene.sql 2020-08-22 16:33 1.9K
refGene.txt.gz 2020-08-22 16:33 82K
refFlat.sql 2020-08-22 16:33 1.7K
refFlat.txt.gz 2020-08-22 16:33 74K
xenoRefGene.sql 2020-08-22 16:33 2.0K
xenoRefGene.txt.gz 2020-08-22 16:33 26M
xenoRefFlat.sql 2020-08-22 16:33 1.7K
xenoRefFlat.txt.gz 2020-08-22 16:33 24M
mrnaOrientInfo.sql 2020-08-22 16:33 1.8K
mrnaOrientInfo.txt.gz 2020-08-22 16:33 80K
refSeqAli.sql 2020-08-22 16:33 2.1K
refSeqAli.txt.gz 2020-08-22 16:33 86K
xenoRefSeqAli.sql 2020-08-22 16:33 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 16:33 26M
gbLoaded.sql 2020-08-22 16:33 1.6K
gbLoaded.txt.gz 2020-08-22 16:33 42K
ensGene.sql 2021-05-25 14:40 1.9K
ensGene.txt.gz 2021-05-25 14:40 2.3M
ensGtp.sql 2021-05-25 14:40 1.4K
ensGtp.txt.gz 2021-05-25 14:40 256K
ensemblToGeneName.sql 2021-05-25 14:40 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:40 14K
ensemblSource.sql 2021-05-25 14:41 1.4K
ensemblSource.txt.gz 2021-05-25 14:41 75K
ensPep.sql 2021-05-25 14:41 1.3K
ensPep.txt.gz 2021-05-25 14:41 6.3M
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 64K
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
tableDescriptions.sql 2024-12-07 02:03 1.5K
tableDescriptions.txt.gz 2024-12-07 02:03 6.4K
tableList.sql 2024-12-08 03:34 1.6K
tableList.txt.gz 2024-12-08 03:34 3.2K
bigFiles.sql 2024-12-08 03:34 1.4K
bigFiles.txt.gz 2024-12-08 03:34 94