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.

---------------------------------------------------------------
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 2021-06-13 03:15 33 grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.txt.gz 2021-06-10 16:54 534 history.txt.gz 2011-04-16 13:40 539 chromInfo.sql 2011-04-16 13:41 1.3K grp.sql 2014-03-02 04:14 1.3K bigFiles.sql 2021-06-13 03:15 1.4K tableDescriptions.sql 2019-07-21 03:43 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 2021-06-13 03:15 1.6K gbLoaded.sql 2020-08-22 17:09 1.6K gold.sql 2011-04-16 13:40 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 refFlat.sql 2020-08-22 17:09 1.7K cpgIslandExtUnmasked.sql 2014-06-01 17:59 1.7K xenoRefFlat.sql 2020-08-22 17:09 1.7K hgFindSpec.sql 2021-06-10 16:54 1.8K estOrientInfo.sql 2016-05-15 11:01 1.8K mrnaOrientInfo.sql 2020-08-22 17:09 1.8K rmsk.sql 2011-04-16 12:18 1.8K simpleRepeat.sql 2011-04-16 13:41 1.9K nestedRepeats.sql 2011-04-16 13:38 1.9K refGene.sql 2020-08-22 17:09 1.9K xenoRefGene.sql 2020-08-22 17:09 1.9K augustusGene.sql 2015-07-26 17:21 1.9K 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 2021-06-10 16:54 2.1K netMm10.sql 2013-10-27 19:46 2.1K all_est.sql 2016-05-15 11:01 2.1K all_mrna.sql 2020-08-22 16:33 2.1K xenoMrna.sql 2016-02-21 21:29 2.1K intronEst.sql 2016-05-15 11:01 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 2021-06-13 03:15 3.1K tableDescriptions.txt.gz 2019-07-21 03:43 5.5K cytoBandIdeo.txt.gz 2013-04-28 19:59 7.5K chromInfo.txt.gz 2011-04-16 13:41 8.5K trackDb.txt.gz 2021-06-10 16:54 27K 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