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:

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:
    See also:

oryCun2.agp.gz - Description of how the assembly was generated from

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

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

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

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
[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:// .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync:// .

Or with wget, all files:
    wget --timestamping 
With wget, a single file:
    wget --timestamping 
        -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 
   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 - est.fa.gz 2019-10-16 12:53 6.9M est.fa.gz.md5 2019-10-16 12:53 44 genes/ 2020-10-02 13:38 - 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 oryCun2.2bit 2009-08-12 10:39 682M oryCun2.agp.gz 2010-04-02 13:40 2.1M oryCun2.chrom.sizes 2009-08-11 11:46 50K 2022-09-08 14:14 579K oryCun2.chromAlias.txt 2022-09-08 14:14 67K oryCun2.fa.gz 2010-04-02 13:57 815M oryCun2.fa.masked.gz 2010-04-02 14:08 482M oryCun2.fa.out.gz 2010-04-02 13:41 140M oryCun2.trf.bed.gz 2010-04-02 13:41 8.5M 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 xenoMrna.fa.gz 2019-10-16 12:48 6.8G xenoMrna.fa.gz.md5 2019-10-16 12:48 49 xenoRefMrna.fa.gz 2019-10-16 12:53 330M xenoRefMrna.fa.gz.md5 2019-10-16 12:53 52