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 -
chainHg38Link.txt.gz 2018-10-02 16:06 750M
chainMm39Link.txt.gz 2020-11-25 04:03 442M
chainMm10Link.txt.gz 2018-10-02 16:10 432M
chainHg38.txt.gz 2018-10-02 16:05 147M
rmsk.txt.gz 2018-10-02 16:12 136M
windowmaskerSdust.txt.gz 2018-10-02 16:13 123M
netHg38.txt.gz 2018-10-02 16:04 65M
chainMm39.txt.gz 2020-11-25 04:00 57M
netMm39.txt.gz 2020-11-25 04:05 54M
netMm10.txt.gz 2018-10-02 16:09 54M
chainMm10.txt.gz 2018-10-02 16:09 53M
xenoRefGene.txt.gz 2018-10-02 16:13 23M
xenoRefFlat.txt.gz 2018-10-02 16:13 21M
xenoRefSeqAli.txt.gz 2018-10-02 16:14 20M
simpleRepeat.txt.gz 2018-10-02 16:13 17M
all_est.txt.gz 2018-10-02 16:04 15M
nestedRepeats.txt.gz 2018-10-02 16:04 14M
ncbiRefSeqPepTable.txt.gz 2021-02-10 16:42 8.9M
intronEst.txt.gz 2018-10-02 16:13 8.4M
estOrientInfo.txt.gz 2018-10-02 16:12 4.3M
ncbiRefSeqPsl.txt.gz 2021-02-10 16:07 3.9M
genscan.txt.gz 2018-10-02 16:13 3.1M
ncbiRefSeq.txt.gz 2021-02-10 16:06 3.0M
ncbiRefSeqPredicted.txt.gz 2021-02-10 16:06 3.0M
augustusGene.txt.gz 2018-10-02 16:04 2.2M
ncbiRefSeqLink.txt.gz 2021-02-10 16:06 1.5M
cpgIslandExtUnmasked.txt.gz 2018-10-02 16:12 942K
gold.txt.gz 2018-10-02 16:13 866K
cpgIslandExt.txt.gz 2018-10-02 16:12 845K
seqNcbiRefSeq.txt.gz 2021-02-10 16:42 771K
gap.txt.gz 2018-10-02 16:12 585K
ncbiRefSeqCds.txt.gz 2021-02-10 16:42 301K
microsat.txt.gz 2018-10-02 16:13 298K
all_mrna.txt.gz 2018-10-02 16:04 223K
refSeqAli.txt.gz 2018-10-02 16:12 91K
refGene.txt.gz 2018-10-02 16:12 84K
mrnaOrientInfo.txt.gz 2018-10-02 16:13 81K
ncbiRefSeqCurated.txt.gz 2021-02-10 16:06 81K
refFlat.txt.gz 2018-10-02 16:12 77K
chromAlias.txt.gz 2018-10-02 16:12 56K
trackDb.txt.gz 2024-04-12 12:08 52K
ucscToINSDC.txt.gz 2018-10-02 16:13 45K
ucscToRefSeq.txt.gz 2018-10-02 16:13 44K
chromInfo.txt.gz 2018-10-02 16:12 34K
trackDb_pushedout.txt.gz 2023-12-05 13:52 31K
cytoBandIdeo.txt.gz 2018-10-02 16:12 31K
tableDescriptions.txt.gz 2024-04-27 02:03 6.2K
tableList.txt.gz 2024-04-28 03:06 3.3K
ncbiRefSeqPsl.sql 2021-02-10 16:07 2.1K
xenoRefSeqAli.sql 2018-10-02 16:14 2.1K
netMm39.sql 2020-11-25 04:05 2.1K
refSeqAli.sql 2018-10-02 16:12 2.1K
intronEst.sql 2018-10-02 16:13 2.1K
all_mrna.sql 2018-10-02 16:04 2.1K
all_est.sql 2018-10-02 16:04 2.1K
netMm10.sql 2018-10-02 16:09 2.1K
netHg38.sql 2018-10-02 16:04 2.1K
trackDb_pushedout.sql 2023-12-05 13:52 2.1K
trackDb.sql 2024-04-12 12:08 2.1K
ncbiRefSeqLink.sql 2021-02-10 16:06 2.0K
ncbiRefSeqPredicted.sql 2021-02-10 16:06 2.0K
ncbiRefSeqCurated.sql 2021-02-10 16:06 2.0K
ncbiRefSeq.sql 2021-02-10 16:06 2.0K
augustusGene.sql 2018-10-02 16:04 1.9K
xenoRefGene.sql 2018-10-02 16:13 1.9K
nestedRepeats.sql 2018-10-02 16:04 1.9K
simpleRepeat.sql 2018-10-02 16:13 1.9K
refGene.sql 2018-10-02 16:12 1.9K
rmsk.sql 2018-10-02 16:12 1.9K
hgFindSpec_pushedout.sql 2023-12-05 13:52 1.8K
hgFindSpec.sql 2024-04-12 12:08 1.8K
mrnaOrientInfo.sql 2018-10-02 16:13 1.8K
estOrientInfo.sql 2018-10-02 16:12 1.8K
chainMm39.sql 2020-11-25 04:00 1.7K
xenoRefFlat.sql 2018-10-02 16:13 1.7K
cpgIslandExtUnmasked.sql 2018-10-02 16:12 1.7K
refFlat.sql 2018-10-02 16:12 1.7K
chainMm10.sql 2018-10-02 16:09 1.7K
chainHg38.sql 2018-10-02 16:05 1.7K
cpgIslandExt.sql 2018-10-02 16:12 1.7K
genscan.sql 2018-10-02 16:13 1.7K
gold.sql 2018-10-02 16:13 1.7K
gap.sql 2018-10-02 16:12 1.6K
tableList.sql 2024-04-28 03:06 1.6K
history.sql 2018-10-02 16:05 1.6K
seqNcbiRefSeq.sql 2021-02-10 16:42 1.6K
chainMm39Link.sql 2020-11-25 04:03 1.6K
chainMm10Link.sql 2018-10-02 16:10 1.5K
chainHg38Link.sql 2018-10-02 16:05 1.5K
cytoBandIdeo.sql 2018-10-02 16:12 1.5K
windowmaskerSdust.sql 2018-10-02 16:13 1.5K
microsat.sql 2018-10-02 16:13 1.5K
extNcbiRefSeq.sql 2021-02-10 16:42 1.5K
tableDescriptions.sql 2024-04-27 02:03 1.5K
ucscToRefSeq.sql 2018-10-02 16:13 1.4K
ucscToINSDC.sql 2018-10-02 16:13 1.4K
chromAlias.sql 2018-10-02 16:12 1.4K
bigFiles.sql 2024-04-28 03:06 1.4K
chromInfo.sql 2018-10-02 16:12 1.4K
ncbiRefSeqPepTable.sql 2021-02-10 16:42 1.4K
ncbiRefSeqCds.sql 2021-02-10 16:42 1.4K
grp.sql 2018-10-02 16:12 1.3K
ncbiRefSeqOther.sql 2021-02-10 16:42 1.3K
gc5BaseBw.sql 2018-10-02 16:12 1.3K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:52 1.1K
hgFindSpec.txt.gz 2024-04-12 12:08 1.1K
history.txt.gz 2018-10-02 16:05 894
grp.txt.gz 2018-10-02 16:12 213
bigFiles.txt.gz 2024-04-28 03:06 95
extNcbiRefSeq.txt.gz 2021-02-10 16:42 91
ncbiRefSeqOther.txt.gz 2021-02-10 16:42 75
gc5BaseBw.txt.gz 2018-10-02 16:12 66