This directory contains a dump of the UCSC genome annotation database for
the Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) assembly of the sheep genome
(oviAri1, ISGC (NCBI project 10709, accession GCA_000005525.1)).
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the International Sheep Genomics Consortium (ISGC).
For more information on the sheep genome, see the project website:
http://www.sheephapmap.org/
http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=33937
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=oviAri1
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/oviAri1/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/oviAri1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/oviAri1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/oviAri1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/oviAri1/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 oviAri1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql oviAri1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
chainHg19.sql 2011-04-16 12:11 1.6K
chainHg19.txt.gz 2011-04-16 12:11 30M
chainMonDom5.sql 2011-04-16 12:12 1.6K
chainMonDom5.txt.gz 2011-04-16 12:12 32M
netBosTau4.sql 2011-04-16 12:13 2.0K
netBosTau4.txt.gz 2011-04-16 12:13 50M
chainMonDom5Link.sql 2011-04-16 12:13 1.5K
chainMonDom5Link.txt.gz 2011-04-16 12:14 105M
ctgPos2.sql 2011-04-16 12:15 1.5K
ctgPos2.txt.gz 2011-04-16 12:15 2.4K
rmsk.sql 2011-04-16 12:18 1.8K
rmsk.txt.gz 2011-04-16 12:19 51M
netEquCab2.sql 2011-04-16 12:19 2.0K
netEquCab2.txt.gz 2011-04-16 12:19 59M
chainHg19Link.sql 2011-04-16 12:20 1.5K
chainHg19Link.txt.gz 2011-04-16 12:21 272M
chainBosTau4Link.sql 2011-04-16 12:24 1.5K
chainBosTau4Link.txt.gz 2011-04-16 12:38 4.1G
gc5Base.sql 2011-04-16 13:26 1.7K
gc5Base.txt.gz 2011-04-16 13:27 11M
gap.sql 2011-04-16 13:27 1.5K
gap.txt.gz 2011-04-16 13:27 34M
chainEquCab2Link.sql 2011-04-16 13:27 1.5K
chainEquCab2Link.txt.gz 2011-04-16 13:29 631M
netHg19.sql 2011-04-16 13:36 2.0K
netHg19.txt.gz 2011-04-16 13:37 57M
nestedRepeats.sql 2011-04-16 13:38 1.9K
nestedRepeats.txt.gz 2011-04-16 13:38 3.4M
chainEquCab2.sql 2011-04-16 13:38 1.6K
chainEquCab2.txt.gz 2011-04-16 13:39 145M
gold.sql 2011-04-16 13:40 1.6K
gold.txt.gz 2011-04-16 13:40 36M
history.sql 2011-04-16 13:40 1.5K
history.txt.gz 2011-04-16 13:40 539
cpgIslandExt.sql 2011-04-16 13:40 1.6K
cpgIslandExt.txt.gz 2011-04-16 13:40 545K
simpleRepeat.sql 2011-04-16 13:41 1.9K
simpleRepeat.txt.gz 2011-04-16 13:41 2.6M
chromInfo.sql 2011-04-16 13:41 1.3K
chromInfo.txt.gz 2011-04-16 13:41 8.5K
netMonDom5.sql 2011-04-16 13:41 2.0K
netMonDom5.txt.gz 2011-04-16 13:41 13M
chainBosTau4.sql 2011-04-16 13:42 1.6K
chainBosTau4.txt.gz 2011-04-16 13:49 2.2G
tRNAs.sql 2012-04-16 03:44 1.7K
tRNAs.txt.gz 2012-04-16 03:44 33K
cytoBandIdeo.sql 2013-04-28 19:59 1.5K
cytoBandIdeo.txt.gz 2013-04-28 19:59 7.5K
chainMm10.sql 2013-10-27 19:46 1.7K
chainMm10.txt.gz 2013-10-27 19:46 14M
chainMm10Link.sql 2013-10-27 19:46 1.5K
chainMm10Link.txt.gz 2013-10-27 19:46 152M
netMm10.sql 2013-10-27 19:46 2.1K
netMm10.txt.gz 2013-10-27 19:47 37M
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 17:59 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 17:59 579K
augustusGene.sql 2015-07-26 17:21 1.9K
augustusGene.txt.gz 2015-07-26 17:21 1.2M
microsat.sql 2015-08-23 23:11 1.5K
microsat.txt.gz 2015-08-23 23:11 32K
xenoMrna.sql 2016-02-21 21:29 2.1K
xenoMrna.txt.gz 2016-02-21 21:30 271M
intronEst.sql 2016-05-15 11:01 2.1K
intronEst.txt.gz 2016-05-15 11:01 6.0M
estOrientInfo.sql 2016-05-15 11:01 1.8K
estOrientInfo.txt.gz 2016-05-15 11:01 3.2M
all_est.sql 2016-05-15 11:01 2.1K
all_est.txt.gz 2016-05-15 11:01 12M
all_mrna.sql 2020-08-22 16:33 2.1K
all_mrna.txt.gz 2020-08-22 16:33 170K
refGene.sql 2020-08-22 17:09 1.9K
refGene.txt.gz 2020-08-22 17:09 75K
refFlat.sql 2020-08-22 17:09 1.7K
refFlat.txt.gz 2020-08-22 17:09 66K
xenoRefGene.sql 2020-08-22 17:09 2.0K
xenoRefGene.txt.gz 2020-08-22 17:09 35M
xenoRefFlat.sql 2020-08-22 17:09 1.7K
xenoRefFlat.txt.gz 2020-08-22 17:09 31M
mrnaOrientInfo.sql 2020-08-22 17:09 1.8K
mrnaOrientInfo.txt.gz 2020-08-22 17:09 58K
refSeqAli.sql 2020-08-22 17:09 2.1K
refSeqAli.txt.gz 2020-08-22 17:09 82K
xenoRefSeqAli.sql 2020-08-22 17:09 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 17:09 33M
gbLoaded.sql 2020-08-22 17:09 1.6K
gbLoaded.txt.gz 2020-08-22 17:09 43K
trackDb_pushedout.sql 2021-08-02 14:31 2.1K
trackDb_pushedout.txt.gz 2021-08-02 14:31 27K
hgFindSpec_pushedout.sql 2021-08-02 14:31 1.8K
hgFindSpec_pushedout.txt.gz 2021-08-02 14:31 544
trackDb.sql 2023-03-28 13:52 2.1K
trackDb.txt.gz 2023-03-28 13:52 28K
hgFindSpec.sql 2023-03-28 13:52 1.8K
hgFindSpec.txt.gz 2023-03-28 13:52 582
tableDescriptions.sql 2024-04-13 02:03 1.5K
tableDescriptions.txt.gz 2024-04-13 02:03 5.7K
tableList.sql 2024-04-14 03:34 1.6K
tableList.txt.gz 2024-04-14 03:34 3.2K
bigFiles.sql 2024-04-14 03:34 1.4K
bigFiles.txt.gz 2024-04-14 03:34 33