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 -
bigFiles.txt.gz 2024-11-17 03:37 33
grp.txt.gz 2014-03-02 04:14 208
history.txt.gz 2011-04-16 13:40 539
hgFindSpec.txt.gz 2023-03-28 13:52 582
chromInfo.sql 2011-04-16 13:41 1.3K
grp.sql 2014-03-02 04:14 1.3K
bigFiles.sql 2024-11-17 03:37 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.4K
chainHg19Link.sql 2011-04-16 12:20 1.5K
ctgPos2.sql 2011-04-16 12:15 1.5K
chainBosTau4Link.sql 2011-04-16 12:24 1.5K
chainEquCab2Link.sql 2011-04-16 13:27 1.5K
chainMonDom5Link.sql 2011-04-16 12:13 1.5K
microsat.sql 2015-08-23 23:11 1.5K
history.sql 2011-04-16 13:40 1.5K
cytoBandIdeo.sql 2013-04-28 19:59 1.5K
gap.sql 2011-04-16 13:27 1.5K
chainMm10Link.sql 2013-10-27 19:46 1.5K
tableList.sql 2024-11-17 03:37 1.6K
gold.sql 2011-04-16 13:40 1.6K
gbLoaded.sql 2020-08-22 17:09 1.6K
cpgIslandExt.sql 2011-04-16 13:40 1.6K
chainHg19.sql 2011-04-16 12:11 1.6K
chainBosTau4.sql 2011-04-16 13:42 1.6K
chainEquCab2.sql 2011-04-16 13:38 1.6K
chainMonDom5.sql 2011-04-16 12:12 1.6K
tRNAs.sql 2012-04-16 03:44 1.7K
gc5Base.sql 2011-04-16 13:26 1.7K
chainMm10.sql 2013-10-27 19:46 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 17:59 1.7K
refFlat.sql 2020-08-22 17:09 1.7K
xenoRefFlat.sql 2020-08-22 17:09 1.7K
hgFindSpec.sql 2023-03-28 13:52 1.8K
estOrientInfo.sql 2016-05-15 11:01 1.8K
rmsk.sql 2011-04-16 12:18 1.8K
mrnaOrientInfo.sql 2020-08-22 17:09 1.8K
simpleRepeat.sql 2011-04-16 13:41 1.9K
nestedRepeats.sql 2011-04-16 13:38 1.9K
augustusGene.sql 2015-07-26 17:21 1.9K
refGene.sql 2020-08-22 17:09 1.9K
xenoRefGene.sql 2020-08-22 17:09 2.0K
netHg19.sql 2011-04-16 13:36 2.0K
netBosTau4.sql 2011-04-16 12:13 2.0K
netEquCab2.sql 2011-04-16 12:19 2.0K
netMonDom5.sql 2011-04-16 13:41 2.0K
trackDb.sql 2023-03-28 13:52 2.1K
netMm10.sql 2013-10-27 19:46 2.1K
all_est.sql 2016-05-15 11:01 2.1K
xenoMrna.sql 2016-02-21 21:29 2.1K
intronEst.sql 2016-05-15 11:01 2.1K
all_mrna.sql 2020-08-22 16:33 2.1K
refSeqAli.sql 2020-08-22 17:09 2.1K
xenoRefSeqAli.sql 2020-08-22 17:09 2.1K
ctgPos2.txt.gz 2011-04-16 12:15 2.4K
tableList.txt.gz 2024-11-17 03:37 3.1K
tableDescriptions.txt.gz 2024-11-16 02:03 5.7K
cytoBandIdeo.txt.gz 2013-04-28 19:59 7.5K
chromInfo.txt.gz 2011-04-16 13:41 8.5K
trackDb.txt.gz 2023-03-28 13:52 28K
microsat.txt.gz 2015-08-23 23:11 32K
tRNAs.txt.gz 2012-04-16 03:44 33K
gbLoaded.txt.gz 2020-08-22 17:09 43K
mrnaOrientInfo.txt.gz 2020-08-22 17:09 58K
refFlat.txt.gz 2020-08-22 17:09 66K
refGene.txt.gz 2020-08-22 17:09 75K
refSeqAli.txt.gz 2020-08-22 17:09 82K
all_mrna.txt.gz 2020-08-22 16:33 170K
cpgIslandExt.txt.gz 2011-04-16 13:40 545K
cpgIslandExtUnmasked.txt.gz 2014-06-01 17:59 579K
augustusGene.txt.gz 2015-07-26 17:21 1.2M
simpleRepeat.txt.gz 2011-04-16 13:41 2.6M
estOrientInfo.txt.gz 2016-05-15 11:01 3.2M
nestedRepeats.txt.gz 2011-04-16 13:38 3.4M
intronEst.txt.gz 2016-05-15 11:01 6.0M
gc5Base.txt.gz 2011-04-16 13:27 11M
all_est.txt.gz 2016-05-15 11:01 12M
netMonDom5.txt.gz 2011-04-16 13:41 13M
chainMm10.txt.gz 2013-10-27 19:46 14M
chainHg19.txt.gz 2011-04-16 12:11 30M
xenoRefFlat.txt.gz 2020-08-22 17:09 31M
chainMonDom5.txt.gz 2011-04-16 12:12 32M
xenoRefSeqAli.txt.gz 2020-08-22 17:09 33M
gap.txt.gz 2011-04-16 13:27 34M
xenoRefGene.txt.gz 2020-08-22 17:09 35M
gold.txt.gz 2011-04-16 13:40 36M
netMm10.txt.gz 2013-10-27 19:47 37M
netBosTau4.txt.gz 2011-04-16 12:13 50M
rmsk.txt.gz 2011-04-16 12:19 51M
netHg19.txt.gz 2011-04-16 13:37 57M
netEquCab2.txt.gz 2011-04-16 12:19 59M
chainMonDom5Link.txt.gz 2011-04-16 12:14 105M
chainEquCab2.txt.gz 2011-04-16 13:39 145M
chainMm10Link.txt.gz 2013-10-27 19:46 152M
xenoMrna.txt.gz 2016-02-21 21:30 271M
chainHg19Link.txt.gz 2011-04-16 12:21 272M
chainEquCab2Link.txt.gz 2011-04-16 13:29 631M
chainBosTau4.txt.gz 2011-04-16 13:49 2.2G
chainBosTau4Link.txt.gz 2011-04-16 12:38 4.1G