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 2024-11-16 02:03 7.3K
tableList.txt.gz 2024-11-17 03:15 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 2024-11-17 03:15 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 2024-11-16 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 2024-11-17 03:15 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 2024-11-17 03:15 73