This directory contains the May 2012 (CerSimSim1.0/cerSim1) assembly of the white rhinoceros genome
(cerSim1, Broad Institute), as well as repeat annotations and GenBank sequences.

For more information about this assembly, please note the NCBI resources:

Files included in this directory:

cerSim1.2bit - contains the complete white rhinoceros/cerSim1 genome sequence
    in the 2bit file format.  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.  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:

cerSim1.agp.gz - Description of how the assembly was generated from

cerSim1.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.

cerSim1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

cerSim1.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.
    April 26 2011 (open-3-3-0) version of RepeatMasker
    RepBase library: RELEASE 20110920

cerSim1.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

md5sum.txt - checksums of files in this directory

mrna.fa.gz - White rhinoceros mRNA from GenBank. This sequence data is updated
    once a week via automatic GenBank updates.

cerSim1.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

cerSim1.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
cerSim1.gc5Base.wig.gz - wiggle database table for the GC Percent track
                    - this is an older standard alternative to the current
                    - bigWig format of the track, sometimes usefull for analysis
cerSim1.gc5Base.wib    - binary data to correspond with the gc5Base.wig file
    see also:
         for a discussion of how to use the wig.gz and .wib files for
         interaction with the GC percent data values

cerSim1.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/cerSim1/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 White rhinoceros 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.

GenBank Data Usage

The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
      Name                          Last modified      Size  Description
Parent Directory - cerSim1.2bit 2012-08-31 13:48 613M cerSim1.agp.gz 2012-10-16 11:14 1.5M cerSim1.chrom.sizes 2012-08-28 15:38 52K 2022-09-08 14:10 748K cerSim1.chromAlias.txt 2022-09-08 14:10 123K cerSim1.fa.gz 2012-10-16 11:28 754M cerSim1.fa.masked.gz 2012-10-16 11:36 471M cerSim1.fa.out.gz 2012-10-16 11:15 114M cerSim1.gc5Base.wib 2019-01-17 14:45 456M cerSim1.gc5Base.wig.gz 2019-01-17 14:45 9.4M cerSim1.gc5Base.wigVarStep.gz 2012-08-28 15:48 1.2G cerSim1.trf.bed.gz 2012-10-16 11:15 2.7M genes/ 2020-02-05 13:46 - md5sum.txt 2019-01-17 15:52 479 mrna.fa.gz 2019-10-15 14:10 1.7M mrna.fa.gz.md5 2019-10-15 14:10 45 xenoRefMrna.fa.gz 2019-10-15 14:10 314M xenoRefMrna.fa.gz.md5 2019-10-15 14:11 52