This directory contains the Apr. 2009 (Broad/oryCun2) assembly of the rabbit genome
(oryCun2, Broad Institute oryCun2 (NCBI project 12819, AAGW00000000)), as well as repeat annotations and GenBank sequences.
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:
oryCun2.2bit - contains the complete rabbit/oryCun2 genome sequence
in the 2bit file format. The utility program, twoBitToFa (available
from the kent src tree), can be used to extract .fa file(s) from
this file. A pre-compiled version of the command line tool can be
found at:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
See also:
http://genome.ucsc.edu/admin/cvs.html
http://genome.ucsc.edu/admin/jk-install.html
oryCun2.agp.gz - Description of how the assembly was generated from
fragments.
oryCun2.fa.gz - "Soft-masked" assembly sequence in one file.
Repeats from RepeatMasker and Tandem Repeats Finder (with period
of 12 or less) are shown in lower case; non-repeating sequence is
shown in upper case.
oryCun2.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
oryCun2.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. *** PLEASE ADD REPEATMASKER VERSION AND LIB VERSION FROM THE DATE THAT REPEATMASKER WAS RUN (MAY BE IN MAKE.DOC)
oryCun2.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format.
est.fa.gz - Rabbit ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Rabbit mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
This sequence data is updated once a week via automatic GenBank
updates.
upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription starts of RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it might be slightly out of sync with
the RefSeq data which is updated daily for most assemblies.
upstream2000.fa.gz - Same as upstream1000, but 2000 bases.
upstream5000.fa.gz - Same as upstream1000, but 5000 bases.
xenoMrna.fa.gz - GenBank mRNAs from species other than that of
the genome. This sequence data is updated once a week via automatic
GenBank updates.
oryCun2.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
oryCun2.chromAlias.txt - sequence name alias file, one line
for each sequence name. First column is sequence name followed by
tab separated alias names.
------------------------------------------------------------------
If you plan to download a large file or multiple files from this
directory, we recommend that you use ftp rather than downloading the
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/oryCun2/bigZips. 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/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/oryCun2/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/oryCun2/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/oryCun2/bigZips/chromFa.tar.gz'
-O chromFa.tar.gz
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
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.
Name Last modified Size Description
Parent Directory -
oryCun2.chrom.sizes 2009-08-11 11:46 50K
oryCun2.2bit 2009-08-12 10:39 682M
oryCun2.agp.gz 2010-04-02 13:40 2.1M
oryCun2.fa.out.gz 2010-04-02 13:41 140M
oryCun2.trf.bed.gz 2010-04-02 13:41 8.5M
oryCun2.fa.gz 2010-04-02 13:57 815M
oryCun2.fa.masked.gz 2010-04-02 14:08 482M
md5sum.txt 2010-05-20 16:29 510
mrna.fa.gz 2019-10-16 12:37 1.1M
mrna.fa.gz.md5 2019-10-16 12:37 45
xenoMrna.fa.gz 2019-10-16 12:48 6.8G
xenoMrna.fa.gz.md5 2019-10-16 12:48 49
est.fa.gz 2019-10-16 12:53 6.9M
est.fa.gz.md5 2019-10-16 12:53 44
xenoRefMrna.fa.gz 2019-10-16 12:53 330M
xenoRefMrna.fa.gz.md5 2019-10-16 12:53 52
refMrna.fa.gz 2019-10-16 12:53 888K
refMrna.fa.gz.md5 2019-10-16 12:53 48
upstream1000.fa.gz 2019-10-16 12:54 14M
upstream1000.fa.gz.md5 2019-10-16 12:54 53
upstream2000.fa.gz 2019-10-16 12:55 27M
upstream2000.fa.gz.md5 2019-10-16 12:55 53
upstream5000.fa.gz 2019-10-16 12:56 77M
upstream5000.fa.gz.md5 2019-10-16 12:56 53
genes/ 2020-10-02 13:38 -
oryCun2.chromAlias.txt 2022-09-08 14:14 67K
oryCun2.chromAlias.bb 2022-09-08 14:14 579K