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.
---------------------------------------------------------------
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;'
-----------------------------------------------------------------------------
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.txt.gz 2013-08-30 12:22 816M
xenoMrna.txt.gz 2020-08-22 15:54 223M
chainHg19.txt.gz 2013-08-30 12:33 189M
rmsk.txt.gz 2013-08-30 12:32 135M
windowmaskerSdust.txt.gz 2013-08-30 12:34 121M
netHg19.txt.gz 2013-08-30 12:31 66M
xenoRefGene.txt.gz 2020-08-22 16:33 26M
xenoRefSeqAli.txt.gz 2020-08-22 16:33 26M
xenoRefFlat.txt.gz 2020-08-22 16:33 24M
simpleRepeat.txt.gz 2013-08-30 12:32 17M
nestedRepeats.txt.gz 2013-08-30 12:32 14M
all_est.txt.gz 2016-05-15 11:01 13M
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:29 8.5M
intronEst.txt.gz 2016-05-15 11:02 8.1M
ensPep.txt.gz 2021-05-25 14:41 6.3M
genscanSubopt.txt.gz 2013-08-30 12:32 5.8M
ncbiRefSeqPsl.txt.gz 2018-02-09 13:49 4.4M
estOrientInfo.txt.gz 2016-05-15 11:01 3.8M
ncbiRefSeq.txt.gz 2018-02-09 13:49 3.3M
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:49 3.2M
genscan.txt.gz 2013-08-30 12:31 3.0M
ensGene.txt.gz 2021-05-25 14:40 2.3M
gold.txt.gz 2013-08-30 12:32 2.3M
augustusGene.txt.gz 2015-07-26 17:21 2.2M
gap.txt.gz 2013-08-30 12:31 1.7M
ncbiRefSeqLink.txt.gz 2018-02-09 13:49 1.6M
seqNcbiRefSeq.txt.gz 2018-08-14 02:29 948K
cpgIslandExtUnmasked.txt.gz 2014-06-01 18:04 918K
cpgIslandExt.txt.gz 2013-08-30 12:32 810K
ncbiRefSeqCds.txt.gz 2018-08-14 02:29 331K
microsat.txt.gz 2015-08-23 23:18 301K
ensGtp.txt.gz 2021-05-25 14:40 256K
all_mrna.txt.gz 2020-08-22 15:54 215K
refSeqAli.txt.gz 2020-08-22 16:33 86K
refGene.txt.gz 2020-08-22 16:33 82K
mrnaOrientInfo.txt.gz 2020-08-22 16:33 80K
ensemblSource.txt.gz 2021-05-25 14:41 75K
refFlat.txt.gz 2020-08-22 16:33 74K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:49 70K
chromAlias.txt.gz 2018-02-18 07:59 61K
ucscToRefSeq.txt.gz 2018-02-18 07:59 47K
gbLoaded.txt.gz 2020-08-22 16:33 42K
trackDb_pushedout.txt.gz 2023-12-05 13:52 35K
trackDb.txt.gz 2023-12-05 13:52 35K
chromInfo.txt.gz 2013-08-30 12:31 34K
cytoBandIdeo.txt.gz 2014-12-14 19:18 32K
ensemblToGeneName.txt.gz 2021-05-25 14:40 14K
animalQtl.txt.gz 2014-06-30 01:24 8.9K
tableDescriptions.txt.gz 2024-04-20 02:03 6.4K
tableList.txt.gz 2024-04-21 03:37 3.4K
xenoRefSeqAli.sql 2020-08-22 16:33 2.1K
ncbiRefSeqPsl.sql 2018-02-09 13:49 2.1K
refSeqAli.sql 2020-08-22 16:33 2.1K
xenoMrna.sql 2020-08-22 15:54 2.1K
all_mrna.sql 2020-08-22 15:54 2.1K
intronEst.sql 2016-05-15 11:02 2.1K
all_est.sql 2016-05-15 11:01 2.1K
netHg19.sql 2013-08-30 12:31 2.1K
trackDb_pushedout.sql 2023-12-05 13:52 2.1K
trackDb.sql 2023-12-05 13:52 2.1K
ncbiRefSeqLink.sql 2018-02-09 13:49 2.0K
ncbiRefSeqPredicted.sql 2018-02-09 13:49 2.0K
ncbiRefSeqCurated.sql 2018-02-09 13:49 2.0K
xenoRefGene.sql 2020-08-22 16:33 2.0K
ncbiRefSeq.sql 2018-02-09 13:49 2.0K
refGene.sql 2020-08-22 16:33 1.9K
ensGene.sql 2021-05-25 14:40 1.9K
augustusGene.sql 2015-07-26 17:21 1.9K
nestedRepeats.sql 2013-08-30 12:32 1.9K
simpleRepeat.sql 2013-08-30 12:32 1.9K
rmsk.sql 2013-08-30 12:31 1.9K
mrnaOrientInfo.sql 2020-08-22 16:33 1.8K
hgFindSpec_pushedout.sql 2023-12-05 13:52 1.8K
estOrientInfo.sql 2016-05-15 11:01 1.8K
hgFindSpec.sql 2023-12-05 13:52 1.8K
xenoRefFlat.sql 2020-08-22 16:33 1.7K
refFlat.sql 2020-08-22 16:33 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 18:04 1.7K
chainHg19.sql 2013-08-30 12:33 1.7K
cpgIslandExt.sql 2013-08-30 12:32 1.7K
genscan.sql 2013-08-30 12:31 1.7K
gold.sql 2013-08-30 12:32 1.7K
gbLoaded.sql 2020-08-22 16:33 1.6K
gap.sql 2013-08-30 12:31 1.6K
tableList.sql 2024-04-21 03:37 1.6K
history.sql 2013-08-30 12:31 1.6K
seqNcbiRefSeq.sql 2018-08-14 02:29 1.6K
genscanSubopt.sql 2013-08-30 12:32 1.6K
chainHg19Link.sql 2013-08-30 12:21 1.5K
cytoBandIdeo.sql 2014-12-14 19:18 1.5K
windowmaskerSdust.sql 2013-08-30 12:33 1.5K
animalQtl.sql 2014-06-30 01:24 1.5K
microsat.sql 2015-08-23 23:18 1.5K
extNcbiRefSeq.sql 2018-08-14 02:29 1.5K
tableDescriptions.sql 2024-04-20 02:03 1.5K
ensGtp.sql 2021-05-25 14:40 1.4K
ucscToRefSeq.sql 2018-02-18 07:59 1.4K
chromAlias.sql 2018-02-18 07:59 1.4K
ensemblToGeneName.sql 2021-05-25 14:40 1.4K
bigFiles.sql 2024-04-21 03:37 1.4K
chromInfo.sql 2013-08-30 12:31 1.4K
ncbiRefSeqPepTable.sql 2018-08-14 02:29 1.4K
ensemblSource.sql 2021-05-25 14:41 1.4K
ncbiRefSeqCds.sql 2018-08-14 02:29 1.4K
grp.sql 2014-03-02 04:14 1.3K
ensPep.sql 2021-05-25 14:41 1.3K
ncbiRefSeqOther.sql 2018-08-14 02:29 1.3K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:52 1.3K
hgFindSpec.txt.gz 2023-12-05 13:52 1.3K
gc5BaseBw.sql 2013-08-30 12:33 1.3K
history.txt.gz 2013-08-30 12:31 392
grp.txt.gz 2014-03-02 04:14 208
bigFiles.txt.gz 2024-04-21 03:37 94
extNcbiRefSeq.txt.gz 2018-08-14 02:29 91
ncbiRefSeqOther.txt.gz 2018-08-14 02:29 75
gc5BaseBw.txt.gz 2013-08-30 12:33 63