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 -
xenoRefSeqAli.txt.gz 2020-08-22 16:33 26M
xenoRefSeqAli.sql 2020-08-22 16:33 2.1K
xenoRefGene.txt.gz 2020-08-22 16:33 26M
xenoRefGene.sql 2020-08-22 16:33 2.0K
xenoRefFlat.txt.gz 2020-08-22 16:33 24M
xenoRefFlat.sql 2020-08-22 16:33 1.7K
xenoMrna.txt.gz 2020-08-22 15:54 223M
xenoMrna.sql 2020-08-22 15:54 2.1K
windowmaskerSdust.txt.gz 2013-08-30 12:34 121M
windowmaskerSdust.sql 2013-08-30 12:33 1.5K
ucscToRefSeq.txt.gz 2018-02-18 07:59 47K
ucscToRefSeq.sql 2018-02-18 07:59 1.4K
trackDb.txt.gz 2024-07-25 09:34 64K
trackDb.sql 2024-07-25 09:34 2.1K
tableList.txt.gz 2024-11-17 03:38 3.2K
tableList.sql 2024-11-17 03:38 1.6K
tableDescriptions.txt.gz 2024-11-16 02:03 6.4K
tableDescriptions.sql 2024-11-16 02:03 1.4K
simpleRepeat.txt.gz 2013-08-30 12:32 17M
simpleRepeat.sql 2013-08-30 12:32 1.9K
seqNcbiRefSeq.txt.gz 2018-08-14 02:29 948K
seqNcbiRefSeq.sql 2018-08-14 02:29 1.6K
rmsk.txt.gz 2013-08-30 12:32 135M
rmsk.sql 2013-08-30 12:31 1.9K
refSeqAli.txt.gz 2020-08-22 16:33 86K
refSeqAli.sql 2020-08-22 16:33 2.1K
refGene.txt.gz 2020-08-22 16:33 82K
refGene.sql 2020-08-22 16:33 1.9K
refFlat.txt.gz 2020-08-22 16:33 74K
refFlat.sql 2020-08-22 16:33 1.7K
netHg19.txt.gz 2013-08-30 12:31 66M
netHg19.sql 2013-08-30 12:31 2.1K
nestedRepeats.txt.gz 2013-08-30 12:32 14M
nestedRepeats.sql 2013-08-30 12:32 1.9K
ncbiRefSeqPsl.txt.gz 2018-02-09 13:49 4.4M
ncbiRefSeqPsl.sql 2018-02-09 13:49 2.1K
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:49 3.2M
ncbiRefSeqPredicted.sql 2018-02-09 13:49 2.0K
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:29 8.5M
ncbiRefSeqPepTable.sql 2018-08-14 02:29 1.4K
ncbiRefSeqOther.txt.gz 2018-08-14 02:29 75
ncbiRefSeqOther.sql 2018-08-14 02:29 1.3K
ncbiRefSeqLink.txt.gz 2018-02-09 13:49 1.6M
ncbiRefSeqLink.sql 2018-02-09 13:49 2.0K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:49 70K
ncbiRefSeqCurated.sql 2018-02-09 13:49 2.0K
ncbiRefSeqCds.txt.gz 2018-08-14 02:29 331K
ncbiRefSeqCds.sql 2018-08-14 02:29 1.4K
ncbiRefSeq.txt.gz 2018-02-09 13:49 3.3M
ncbiRefSeq.sql 2018-02-09 13:49 2.0K
mrnaOrientInfo.txt.gz 2020-08-22 16:33 80K
mrnaOrientInfo.sql 2020-08-22 16:33 1.8K
microsat.txt.gz 2015-08-23 23:18 301K
microsat.sql 2015-08-23 23:18 1.5K
intronEst.txt.gz 2016-05-15 11:02 8.1M
intronEst.sql 2016-05-15 11:02 2.1K
history.txt.gz 2013-08-30 12:31 392
history.sql 2013-08-30 12:31 1.6K
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
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 2013-08-30 12:32 2.3M
gold.sql 2013-08-30 12:32 1.7K
genscanSubopt.txt.gz 2013-08-30 12:32 5.8M
genscanSubopt.sql 2013-08-30 12:32 1.6K
genscan.txt.gz 2013-08-30 12:31 3.0M
genscan.sql 2013-08-30 12:31 1.7K
gc5BaseBw.txt.gz 2013-08-30 12:33 63
gc5BaseBw.sql 2013-08-30 12:33 1.3K
gbLoaded.txt.gz 2020-08-22 16:33 42K
gbLoaded.sql 2020-08-22 16:33 1.6K
gap.txt.gz 2013-08-30 12:31 1.7M
gap.sql 2013-08-30 12:31 1.6K
extNcbiRefSeq.txt.gz 2018-08-14 02:29 91
extNcbiRefSeq.sql 2018-08-14 02:29 1.5K
estOrientInfo.txt.gz 2016-05-15 11:01 3.8M
estOrientInfo.sql 2016-05-15 11:01 1.8K
ensemblToGeneName.txt.gz 2021-05-25 14:40 14K
ensemblToGeneName.sql 2021-05-25 14:40 1.4K
ensemblSource.txt.gz 2021-05-25 14:41 75K
ensemblSource.sql 2021-05-25 14:41 1.4K
ensPep.txt.gz 2021-05-25 14:41 6.3M
ensPep.sql 2021-05-25 14:41 1.3K
ensGtp.txt.gz 2021-05-25 14:40 256K
ensGtp.sql 2021-05-25 14:40 1.4K
ensGene.txt.gz 2021-05-25 14:40 2.3M
ensGene.sql 2021-05-25 14:40 1.9K
cytoBandIdeo.txt.gz 2014-12-14 19:18 32K
cytoBandIdeo.sql 2014-12-14 19:18 1.5K
cpgIslandExtUnmasked.txt.gz 2014-06-01 18:04 918K
cpgIslandExtUnmasked.sql 2014-06-01 18:04 1.7K
cpgIslandExt.txt.gz 2013-08-30 12:32 810K
cpgIslandExt.sql 2013-08-30 12:32 1.7K
chromInfo.txt.gz 2013-08-30 12:31 34K
chromInfo.sql 2013-08-30 12:31 1.4K
chromAlias.txt.gz 2018-02-18 07:59 61K
chromAlias.sql 2018-02-18 07:59 1.4K
chainHg19Link.txt.gz 2013-08-30 12:22 816M
chainHg19Link.sql 2013-08-30 12:21 1.5K
chainHg19.txt.gz 2013-08-30 12:33 189M
chainHg19.sql 2013-08-30 12:33 1.7K
bigFiles.txt.gz 2024-11-17 03:38 94
bigFiles.sql 2024-11-17 03:38 1.4K
augustusGene.txt.gz 2015-07-26 17:21 2.2M
augustusGene.sql 2015-07-26 17:21 1.9K
animalQtl.txt.gz 2014-06-30 01:24 8.9K
animalQtl.sql 2014-06-30 01:24 1.5K
all_mrna.txt.gz 2020-08-22 15:54 215K
all_mrna.sql 2020-08-22 15:54 2.1K
all_est.txt.gz 2016-05-15 11:01 13M
all_est.sql 2016-05-15 11:01 2.1K