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