This directory contains a dump of the UCSC genome annotation database for
the Apr. 2009 (Broad/oryCun2) assembly of the rabbit genome (oryCun2, Broad Institute oryCun2 (NCBI project 12819, AAGW00000000)).
The annotations were generated by UCSC and collaborators worldwide.

This assembly was produced by the Broad Institute of MIT and Harvard.
For more information on the rabbit genome, see the project website:
http://www.broadinstitute.org/science/projects/mammals-models/rabbit/rabbit-genome-sequencing-project

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=oryCun2
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/oryCun2/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/oryCun2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/oryCun2/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/oryCun2/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/oryCun2/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 oryCun2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql oryCun2 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

The Rabbit sequence is made freely available before scientific publication 
with the following understanding:

   1. The data may be freely downloaded, used in analyses, and repackaged in 
      databases.
   2. Users are free to use the data in scientific papers analyzing particular 
      genes and regions if the provider of these data (The Broad Institute) is 
      properly acknowledged.
   3. The center producing the data reserves the right to publish the initial 
      large-scale analyses of the data set, including large-scale identification 
      of regions of evolutionary conservation and large-scale genomic assembly. 
      Large-scale refers to regions with size on the order of a chromosome (that 
      is, 30 Mb or more).
   4. Any redistribution of the data should carry this notice. 1. The data may 
      be freely downloaded, used in analyses, and repackaged in databases.

All the files and tables in this directory are freely usable for any purpose.

      Name                        Last modified      Size  Description
Parent Directory - all_est.sql 2016-05-15 10:55 2.1K all_est.txt.gz 2016-05-15 10:55 1.3M all_mrna.sql 2020-08-19 23:14 2.1K all_mrna.txt.gz 2020-08-19 23:14 259K augustusGene.sql 2015-07-26 17:21 1.9K augustusGene.txt.gz 2015-07-26 17:21 2.3M bigFiles.sql 2021-05-16 03:03 1.4K bigFiles.txt.gz 2021-05-16 03:03 73 blastHg18KG.sql 2010-05-02 15:15 2.1K blastHg18KG.txt.gz 2010-05-02 15:15 4.2M chainCavPor3.sql 2010-04-26 16:44 1.6K chainCavPor3.txt.gz 2010-04-26 16:45 515M chainCavPor3Link.sql 2010-04-26 16:19 1.5K chainCavPor3Link.txt.gz 2010-04-26 16:23 1.9G chainHg19.sql 2010-04-26 16:14 1.8K chainHg19.txt.gz 2010-04-26 16:15 126M chainHg19Link.sql 2010-04-26 16:47 1.5K chainHg19Link.txt.gz 2010-04-26 16:48 673M chainMm10.sql 2013-10-27 19:25 1.7K chainMm10.txt.gz 2013-10-27 19:26 78M chainMm10Link.sql 2013-10-27 19:26 1.5K chainMm10Link.txt.gz 2013-10-27 19:26 481M chainMm39.sql 2020-11-25 04:22 1.7K chainMm39.txt.gz 2020-11-25 04:22 64M chainMm39Link.sql 2020-11-25 04:25 1.6K chainMm39Link.txt.gz 2020-11-25 04:25 437M chainMonDom5.sql 2010-04-26 16:16 1.6K chainMonDom5.txt.gz 2010-04-26 16:17 330M chainMonDom5Link.sql 2010-04-26 16:37 1.5K chainMonDom5Link.txt.gz 2010-04-26 16:39 948M chainRn6.sql 2017-03-27 19:31 1.7K chainRn6.txt.gz 2017-03-27 19:32 81M chainRn6Link.sql 2017-03-27 19:34 1.5K chainRn6Link.txt.gz 2017-03-27 19:40 507M chromAlias.sql 2018-08-05 08:35 1.4K chromAlias.txt.gz 2018-08-05 08:35 17K chromInfo.sql 2010-04-26 16:57 1.3K chromInfo.txt.gz 2010-04-26 16:57 18K cpgIslandExt.sql 2017-07-16 06:16 1.7K cpgIslandExt.txt.gz 2017-07-16 06:16 1.4M cpgIslandExtUnmasked.sql 2017-07-16 06:16 1.7K cpgIslandExtUnmasked.txt.gz 2017-07-16 06:16 2.1M ctgPos2.sql 2010-04-26 16:44 1.5K ctgPos2.txt.gz 2010-04-26 16:44 36K cytoBandIdeo.sql 2013-04-28 19:40 1.5K cytoBandIdeo.txt.gz 2013-04-28 19:40 18K ensGene.sql 2020-08-31 15:46 1.9K ensGene.txt.gz 2020-08-31 15:46 2.9M ensGtp.sql 2020-08-31 15:46 1.4K ensGtp.txt.gz 2020-08-31 15:46 518K ensPep.sql 2020-08-31 16:22 1.3K ensPep.txt.gz 2020-08-31 16:22 14M ensemblSource.sql 2020-08-31 16:22 1.4K ensemblSource.txt.gz 2020-08-31 16:22 159K ensemblToGeneName.sql 2020-08-31 15:46 1.4K ensemblToGeneName.txt.gz 2020-08-31 15:46 208K estOrientInfo.sql 2016-05-15 10:55 1.8K estOrientInfo.txt.gz 2016-05-15 10:55 416K extNcbiRefSeq.sql 2020-05-10 03:28 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:28 91 gap.sql 2010-04-26 16:19 1.6K gap.txt.gz 2010-04-26 16:19 1.1M gbLoaded.sql 2020-08-19 23:41 1.6K gbLoaded.txt.gz 2020-08-19 23:41 110K gc5Base.sql 2010-04-26 16:55 1.9K gc5Base.txt.gz 2010-04-26 16:55 11M geneid.sql 2015-11-22 19:57 1.9K geneid.txt.gz 2015-11-22 19:57 2.4M genscan.sql 2013-12-10 03:29 1.7K genscan.txt.gz 2013-12-10 03:29 3.5M gold.sql 2010-04-26 16:56 1.7K gold.txt.gz 2010-04-26 16:56 1.4M grp.sql 2014-03-02 04:14 1.4K grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.sql 2021-03-31 13:53 1.8K hgFindSpec.txt.gz 2021-03-31 13:53 1.3K history.sql 2010-04-26 16:52 1.6K history.txt.gz 2010-04-26 16:52 828 intronEst.sql 2016-05-15 10:55 2.1K intronEst.txt.gz 2016-05-15 10:55 718K microsat.sql 2015-08-23 22:48 1.5K microsat.txt.gz 2015-08-23 22:48 595K mrnaOrientInfo.sql 2020-08-19 23:41 1.8K mrnaOrientInfo.txt.gz 2020-08-19 23:41 82K ncbiRefSeq.sql 2020-05-10 03:28 1.9K ncbiRefSeq.txt.gz 2020-05-10 03:28 2.7M ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K ncbiRefSeqCds.txt.gz 2020-05-10 03:28 264K ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 121K ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.3M ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75 ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 8.8M ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.6M ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 3.3M nestedRepeats.sql 2010-04-26 16:34 2.0K nestedRepeats.txt.gz 2010-04-26 16:34 13M netCavPor3.sql 2010-04-26 16:54 2.0K netCavPor3.txt.gz 2010-04-26 16:54 64M netHg19.sql 2010-04-26 16:53 2.3K netHg19.txt.gz 2010-04-26 16:54 58M netMm10.sql 2013-10-27 19:28 2.1K netMm10.txt.gz 2013-10-27 19:28 49M netMm39.sql 2020-11-25 04:28 2.1K netMm39.txt.gz 2020-11-25 04:28 49M netMonDom5.sql 2010-04-26 16:57 2.0K netMonDom5.txt.gz 2010-04-26 16:57 15M netRn6.sql 2017-03-27 20:00 2.1K netRn6.txt.gz 2017-03-27 20:01 48M quality.sql 2010-04-26 16:15 1.9K quality.txt.gz 2010-04-26 16:15 45M refFlat.sql 2020-08-19 23:41 1.7K refFlat.txt.gz 2020-08-19 23:41 128K refGene.sql 2020-08-19 23:41 1.9K refGene.txt.gz 2020-08-19 23:41 139K refSeqAli.sql 2020-08-19 23:41 2.1K refSeqAli.txt.gz 2020-08-19 23:41 146K rmsk.sql 2010-04-26 16:18 2.0K rmsk.txt.gz 2010-04-26 16:18 118M seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:28 662K simpleRepeat.sql 2010-04-26 16:56 2.0K simpleRepeat.txt.gz 2010-04-26 16:56 21M tRNAs.sql 2012-04-23 07:55 1.7K tRNAs.txt.gz 2012-04-23 07:55 13K tableDescriptions.sql 2021-03-13 06:37 1.4K tableDescriptions.txt.gz 2021-03-13 06:37 7.2K tableList.sql 2021-05-16 03:03 1.6K tableList.txt.gz 2021-05-16 03:03 4.4K trackDb.sql 2021-03-31 13:53 2.1K trackDb.txt.gz 2021-03-31 13:53 49K ucscToEnsembl.sql 2011-11-14 02:33 1.3K ucscToEnsembl.txt.gz 2011-11-14 02:33 15K ucscToINSDC.sql 2013-09-15 17:23 1.4K ucscToINSDC.txt.gz 2013-09-15 17:23 27K xenoMrna.sql 2020-08-19 23:14 2.1K xenoMrna.txt.gz 2020-08-19 23:14 347M xenoRefFlat.sql 2020-08-19 23:41 1.7K xenoRefFlat.txt.gz 2020-08-19 23:41 31M xenoRefGene.sql 2020-08-19 23:41 1.9K xenoRefGene.txt.gz 2020-08-19 23:41 34M xenoRefSeqAli.sql 2020-08-19 23:41 2.1K xenoRefSeqAli.txt.gz 2020-08-19 23:41 35M