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 - chainCavPor3Link.txt.gz 2010-04-26 16:23 1.9G chainMonDom5Link.txt.gz 2010-04-26 16:39 948M chainHg19Link.txt.gz 2010-04-26 16:48 673M chainCavPor3.txt.gz 2010-04-26 16:45 515M chainRn6Link.txt.gz 2017-03-27 19:40 507M chainMm10Link.txt.gz 2013-10-27 19:26 481M chainMm39Link.txt.gz 2020-11-25 04:25 437M xenoMrna.txt.gz 2020-08-19 23:14 347M chainMonDom5.txt.gz 2010-04-26 16:17 330M chainHg19.txt.gz 2010-04-26 16:15 126M rmsk.txt.gz 2010-04-26 16:18 118M chainRn6.txt.gz 2017-03-27 19:32 81M chainMm10.txt.gz 2013-10-27 19:26 78M chainMm39.txt.gz 2020-11-25 04:22 64M netCavPor3.txt.gz 2010-04-26 16:54 64M netHg19.txt.gz 2010-04-26 16:54 58M netMm39.txt.gz 2020-11-25 04:28 49M netMm10.txt.gz 2013-10-27 19:28 49M netRn6.txt.gz 2017-03-27 20:01 48M quality.txt.gz 2010-04-26 16:15 45M xenoRefSeqAli.txt.gz 2020-08-19 23:41 35M xenoRefGene.txt.gz 2020-08-19 23:41 34M xenoRefFlat.txt.gz 2020-08-19 23:41 31M simpleRepeat.txt.gz 2010-04-26 16:56 21M netMonDom5.txt.gz 2010-04-26 16:57 15M ensPep.txt.gz 2021-05-25 14:43 14M nestedRepeats.txt.gz 2010-04-26 16:34 13M gc5Base.txt.gz 2010-04-26 16:55 11M ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 8.8M blastHg18KG.txt.gz 2010-05-02 15:15 4.2M genscan.txt.gz 2013-12-10 03:29 3.5M ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 3.3M ensGene.txt.gz 2021-05-25 14:41 2.9M ncbiRefSeq.txt.gz 2020-05-10 03:28 2.7M ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.6M geneid.txt.gz 2015-11-22 19:57 2.4M augustusGene.txt.gz 2015-07-26 17:21 2.3M cpgIslandExtUnmasked.txt.gz 2017-07-16 06:16 2.1M gold.txt.gz 2010-04-26 16:56 1.4M cpgIslandExt.txt.gz 2017-07-16 06:16 1.4M all_est.txt.gz 2016-05-15 10:55 1.3M ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.3M gap.txt.gz 2010-04-26 16:19 1.1M intronEst.txt.gz 2016-05-15 10:55 718K seqNcbiRefSeq.txt.gz 2020-05-10 03:28 662K microsat.txt.gz 2015-08-23 22:48 595K ensGtp.txt.gz 2021-05-25 14:41 519K estOrientInfo.txt.gz 2016-05-15 10:55 416K ncbiRefSeqCds.txt.gz 2020-05-10 03:28 264K all_mrna.txt.gz 2020-08-19 23:14 259K ensemblToGeneName.txt.gz 2021-05-25 14:41 207K ensemblSource.txt.gz 2021-05-25 14:43 159K refSeqAli.txt.gz 2020-08-19 23:41 146K refGene.txt.gz 2020-08-19 23:41 139K refFlat.txt.gz 2020-08-19 23:41 128K ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 121K gbLoaded.txt.gz 2020-08-19 23:41 110K mrnaOrientInfo.txt.gz 2020-08-19 23:41 82K trackDb.txt.gz 2024-01-31 15:13 55K ctgPos2.txt.gz 2010-04-26 16:44 36K ucscToINSDC.txt.gz 2013-09-15 17:23 27K chromInfo.txt.gz 2010-04-26 16:57 18K cytoBandIdeo.txt.gz 2013-04-28 19:40 18K chromAlias.txt.gz 2018-08-05 08:35 17K ucscToEnsembl.txt.gz 2011-11-14 02:33 15K tRNAs.txt.gz 2012-04-23 07:55 13K tableDescriptions.txt.gz 2024-10-05 02:03 7.3K tableList.txt.gz 2024-10-06 03:09 4.4K netHg19.sql 2010-04-26 16:53 2.3K xenoRefSeqAli.sql 2020-08-19 23:41 2.1K refSeqAli.sql 2020-08-19 23:41 2.1K xenoMrna.sql 2020-08-19 23:14 2.1K all_mrna.sql 2020-08-19 23:14 2.1K ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K netMm39.sql 2020-11-25 04:28 2.1K intronEst.sql 2016-05-15 10:55 2.1K all_est.sql 2016-05-15 10:55 2.1K netMm10.sql 2013-10-27 19:28 2.1K netRn6.sql 2017-03-27 20:00 2.1K trackDb.sql 2024-01-31 15:13 2.1K blastHg18KG.sql 2010-05-02 15:15 2.1K simpleRepeat.sql 2010-04-26 16:56 2.0K netMonDom5.sql 2010-04-26 16:57 2.0K netCavPor3.sql 2010-04-26 16:54 2.0K nestedRepeats.sql 2010-04-26 16:34 2.0K ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K rmsk.sql 2010-04-26 16:18 2.0K ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K xenoRefGene.sql 2020-08-19 23:41 2.0K ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K refGene.sql 2020-08-19 23:41 1.9K ensGene.sql 2021-05-25 14:41 1.9K augustusGene.sql 2015-07-26 17:21 1.9K ncbiRefSeq.sql 2020-05-10 03:28 1.9K geneid.sql 2015-11-22 19:57 1.9K quality.sql 2010-04-26 16:15 1.9K gc5Base.sql 2010-04-26 16:55 1.9K mrnaOrientInfo.sql 2020-08-19 23:41 1.8K chainHg19.sql 2010-04-26 16:14 1.8K estOrientInfo.sql 2016-05-15 10:55 1.8K hgFindSpec.sql 2024-01-31 15:13 1.8K xenoRefFlat.sql 2020-08-19 23:41 1.7K refFlat.sql 2020-08-19 23:41 1.7K chainMm39.sql 2020-11-25 04:22 1.7K gold.sql 2010-04-26 16:56 1.7K cpgIslandExtUnmasked.sql 2017-07-16 06:16 1.7K chainMm10.sql 2013-10-27 19:25 1.7K chainRn6.sql 2017-03-27 19:31 1.7K cpgIslandExt.sql 2017-07-16 06:16 1.7K tRNAs.sql 2012-04-23 07:55 1.7K genscan.sql 2013-12-10 03:29 1.7K chainMonDom5.sql 2010-04-26 16:16 1.6K chainCavPor3.sql 2010-04-26 16:44 1.6K gap.sql 2010-04-26 16:19 1.6K gbLoaded.sql 2020-08-19 23:41 1.6K tableList.sql 2024-10-06 03:09 1.6K chainMm39Link.sql 2020-11-25 04:25 1.6K history.sql 2010-04-26 16:52 1.6K seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K chainMm10Link.sql 2013-10-27 19:26 1.5K chainHg19Link.sql 2010-04-26 16:47 1.5K ctgPos2.sql 2010-04-26 16:44 1.5K chainRn6Link.sql 2017-03-27 19:34 1.5K cytoBandIdeo.sql 2013-04-28 19:40 1.5K microsat.sql 2015-08-23 22:48 1.5K chainMonDom5Link.sql 2010-04-26 16:37 1.5K chainCavPor3Link.sql 2010-04-26 16:19 1.5K ensGtp.sql 2021-05-25 14:41 1.4K extNcbiRefSeq.sql 2020-05-10 03:28 1.4K tableDescriptions.sql 2024-10-05 02:03 1.4K ucscToINSDC.sql 2013-09-15 17:23 1.4K chromAlias.sql 2018-08-05 08:35 1.4K ensemblToGeneName.sql 2021-05-25 14:41 1.4K grp.sql 2014-03-02 04:14 1.4K hgFindSpec.txt.gz 2024-01-31 15:13 1.4K bigFiles.sql 2024-10-06 03:09 1.4K ensemblSource.sql 2021-05-25 14:43 1.4K ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K ensPep.sql 2021-05-25 14:43 1.3K ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K chromInfo.sql 2010-04-26 16:57 1.3K ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K ucscToEnsembl.sql 2011-11-14 02:33 1.3K history.txt.gz 2010-04-26 16:52 828 grp.txt.gz 2014-03-02 04:14 208 extNcbiRefSeq.txt.gz 2020-05-10 03:28 91 ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75 bigFiles.txt.gz 2024-10-06 03:09 73