This directory contains a dump of the UCSC genome annotation database for the
Nov. 2015 (Oar_v4.0/oviAri4) assembly of the sheep genome
(oviAri4, International Sheep Genome Consortium) .
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
https://www.ncbi.nlm.nih.gov/genome/83
https://www.ncbi.nlm.nih.gov/genome/assembly/585171
https://www.ncbi.nlm.nih.gov/bioproject/169880
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=oviAri4
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.soe.ucsc.edu, then go to
the directory goldenPath/oviAri4/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.soe.ucsc.edu/goldenPath/oviAri4/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/oviAri4/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/oviAri4/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/oviAri4/database/gc5Base.txt.gz'
-O gc5Base.txt.gz
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 oviAri4 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql oviAri4 --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 -
all_est.sql 2018-10-02 16:04 2.1K
all_est.txt.gz 2018-10-02 16:04 15M
nestedRepeats.sql 2018-10-02 16:04 1.9K
nestedRepeats.txt.gz 2018-10-02 16:04 14M
all_mrna.sql 2018-10-02 16:04 2.1K
all_mrna.txt.gz 2018-10-02 16:04 223K
augustusGene.sql 2018-10-02 16:04 1.9K
augustusGene.txt.gz 2018-10-02 16:04 2.2M
netHg38.sql 2018-10-02 16:04 2.1K
netHg38.txt.gz 2018-10-02 16:04 65M
chainHg38.sql 2018-10-02 16:05 1.7K
chainHg38.txt.gz 2018-10-02 16:05 147M
chainHg38Link.sql 2018-10-02 16:05 1.5K
history.sql 2018-10-02 16:05 1.6K
history.txt.gz 2018-10-02 16:05 894
chainHg38Link.txt.gz 2018-10-02 16:06 750M
netMm10.sql 2018-10-02 16:09 2.1K
netMm10.txt.gz 2018-10-02 16:09 54M
chainMm10.sql 2018-10-02 16:09 1.7K
chainMm10.txt.gz 2018-10-02 16:09 53M
chainMm10Link.sql 2018-10-02 16:10 1.5K
chainMm10Link.txt.gz 2018-10-02 16:10 432M
chromAlias.sql 2018-10-02 16:12 1.4K
chromAlias.txt.gz 2018-10-02 16:12 56K
chromInfo.sql 2018-10-02 16:12 1.4K
chromInfo.txt.gz 2018-10-02 16:12 34K
cpgIslandExt.sql 2018-10-02 16:12 1.7K
cpgIslandExt.txt.gz 2018-10-02 16:12 845K
refFlat.sql 2018-10-02 16:12 1.7K
refFlat.txt.gz 2018-10-02 16:12 77K
cpgIslandExtUnmasked.sql 2018-10-02 16:12 1.7K
cpgIslandExtUnmasked.txt.gz 2018-10-02 16:12 942K
cytoBandIdeo.sql 2018-10-02 16:12 1.5K
cytoBandIdeo.txt.gz 2018-10-02 16:12 31K
estOrientInfo.sql 2018-10-02 16:12 1.8K
grp.sql 2018-10-02 16:12 1.3K
grp.txt.gz 2018-10-02 16:12 213
estOrientInfo.txt.gz 2018-10-02 16:12 4.3M
gap.sql 2018-10-02 16:12 1.6K
gap.txt.gz 2018-10-02 16:12 585K
gc5BaseBw.sql 2018-10-02 16:12 1.3K
gc5BaseBw.txt.gz 2018-10-02 16:12 66
refGene.sql 2018-10-02 16:12 1.9K
refGene.txt.gz 2018-10-02 16:12 84K
refSeqAli.sql 2018-10-02 16:12 2.1K
refSeqAli.txt.gz 2018-10-02 16:12 91K
rmsk.sql 2018-10-02 16:12 1.9K
rmsk.txt.gz 2018-10-02 16:12 136M
genscan.sql 2018-10-02 16:13 1.7K
genscan.txt.gz 2018-10-02 16:13 3.1M
gold.sql 2018-10-02 16:13 1.7K
gold.txt.gz 2018-10-02 16:13 866K
intronEst.sql 2018-10-02 16:13 2.1K
intronEst.txt.gz 2018-10-02 16:13 8.4M
simpleRepeat.sql 2018-10-02 16:13 1.9K
simpleRepeat.txt.gz 2018-10-02 16:13 17M
microsat.sql 2018-10-02 16:13 1.5K
microsat.txt.gz 2018-10-02 16:13 298K
mrnaOrientInfo.sql 2018-10-02 16:13 1.8K
mrnaOrientInfo.txt.gz 2018-10-02 16:13 81K
ucscToINSDC.sql 2018-10-02 16:13 1.4K
ucscToINSDC.txt.gz 2018-10-02 16:13 45K
ucscToRefSeq.sql 2018-10-02 16:13 1.4K
ucscToRefSeq.txt.gz 2018-10-02 16:13 44K
windowmaskerSdust.sql 2018-10-02 16:13 1.5K
windowmaskerSdust.txt.gz 2018-10-02 16:13 123M
xenoRefFlat.sql 2018-10-02 16:13 1.7K
xenoRefFlat.txt.gz 2018-10-02 16:13 21M
xenoRefGene.sql 2018-10-02 16:13 1.9K
xenoRefGene.txt.gz 2018-10-02 16:13 23M
xenoRefSeqAli.sql 2018-10-02 16:14 2.1K
xenoRefSeqAli.txt.gz 2018-10-02 16:14 20M
chainMm39.sql 2020-11-25 04:00 1.7K
chainMm39.txt.gz 2020-11-25 04:00 57M
chainMm39Link.sql 2020-11-25 04:03 1.6K
chainMm39Link.txt.gz 2020-11-25 04:03 442M
netMm39.sql 2020-11-25 04:05 2.1K
netMm39.txt.gz 2020-11-25 04:05 54M
ncbiRefSeq.sql 2021-02-10 16:06 2.0K
ncbiRefSeq.txt.gz 2021-02-10 16:06 3.0M
ncbiRefSeqCurated.sql 2021-02-10 16:06 2.0K
ncbiRefSeqCurated.txt.gz 2021-02-10 16:06 81K
ncbiRefSeqPredicted.sql 2021-02-10 16:06 2.0K
ncbiRefSeqPredicted.txt.gz 2021-02-10 16:06 3.0M
ncbiRefSeqLink.sql 2021-02-10 16:06 2.0K
ncbiRefSeqLink.txt.gz 2021-02-10 16:06 1.5M
ncbiRefSeqPsl.sql 2021-02-10 16:07 2.1K
ncbiRefSeqPsl.txt.gz 2021-02-10 16:07 3.9M
ncbiRefSeqOther.sql 2021-02-10 16:42 1.3K
ncbiRefSeqOther.txt.gz 2021-02-10 16:42 75
ncbiRefSeqCds.sql 2021-02-10 16:42 1.4K
ncbiRefSeqCds.txt.gz 2021-02-10 16:42 301K
ncbiRefSeqPepTable.sql 2021-02-10 16:42 1.4K
ncbiRefSeqPepTable.txt.gz 2021-02-10 16:42 8.9M
extNcbiRefSeq.sql 2021-02-10 16:42 1.5K
extNcbiRefSeq.txt.gz 2021-02-10 16:42 91
seqNcbiRefSeq.sql 2021-02-10 16:42 1.6K
seqNcbiRefSeq.txt.gz 2021-02-10 16:42 771K
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 67K
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 1.1K
tableDescriptions.sql 2024-12-07 02:03 1.5K
tableDescriptions.txt.gz 2024-12-07 02:03 6.2K
tableList.sql 2024-12-08 03:05 1.6K
tableList.txt.gz 2024-12-08 03:05 3.1K
bigFiles.sql 2024-12-08 03:05 1.4K
bigFiles.txt.gz 2024-12-08 03:05 95