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