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Dr. Christoph Mayer
Animal Ecology, Evolution and Biodiversity, Faculty of Biological Sciences and Biotechnology
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Animal Ecology, Evolution and Biodiversity » Members » Dr. Christoph Mayer » Software
pix pix Software written by Christoph Mayer

    Phobos - a tandem repeat search tool for complete genomes - Version 3.3.12 is now available (September 2010) - Geneious plugin needs version 3.3.10 or higher

    (Opens a pop-up window, so pop-ups should not be supressed)

    Phobos is a highly accurate and fast search tool for
    - DNA-microsatellites,
    - DNA-minisatellites and
    - DNA-satellites

    Two of our recent papers that use Phobos:
    • Leese, F, Mayer, C, and Held, C (2008): Isolation of microsatellites from unknown genomes using known genomes as enrichment templates. Limnology and Oceanography: Methods 7, 412-426. (Abstract)

    • Mayer C, Leese F, Tollrian R (2010): Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach. BMC Genomics (Abstract, PDF).

    Phobos is a multi platform program (Mac, Linux, Windows, and maybe others, such as Solaris, upon request)
    that comes in two versions:
    - user friendly GUI (graphical user interface) program
    - easily scriptable CL (command-line) program.

    Visualisation of tandem repeats and user friendly primer design
    Phobos has been integrated into the following molecular biology analysis tools, which in particular offer a convenient interfaces for designing flanking primers of microsatellites.
    Commercial users always need to obtain a user license for Phobos directly from the author Christoph Mayer.

    • STAMP: Microsatellite marker design extension for the Staden package
      Reference:
      Kraemer, L., Beszteri, B., Gaebler-Schwarz, S., Held, C., Leese, F., Mayer, C., Poehlmann, K. & Frickenhaus, S. (2009)
      STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
      BMC Bioinformatics 10:41.

    • Phobos plugin for Geneious.
      Geneious is a commercial and easy to use DNA and protein sequence analysis tool.
      In order to use the tandem repeat detection capabilities of Phobos in Geneious one has to install the command-line version of Phobos (version 3.3.10 or higher) as well as the Phobos plugin.

    Phobos has the following main features:
    • it uses an exact, in particular non-probabilistic search algorithm,
    • it can search for perfect satellites with a pattern size of 1 - 10000 bp in complete genomes,
    • it can search for imperfect satellites in complete genomes in the pattern size range 1 - 50 bp with a high detection and alignment quality, and for patterns with a size of 10000 bp with a reduced detection and alignment quality.
    • it uses the alignment score as an optimality criterion to decide whether to extend a satellite up or downstream,
    • it detects and reports overlapping satellites,
    • it tries to extend satellites up and down stream to obtain highly accurate results which are mostly independent of the search direction,
    • it is able to find alternative alignments with different units for the same satellite,
    • it can report repeats in a variety of different output formats, including formats that show flanking regions or the alignment of the repeat region with the repeat pattern.

    When developing a DNA-satellite search tool, two main problems occur:
    The program should
    (1) detect imperfect repeats, i.e. repeats with mismatches and indels,
    (2) be able to cope with repeats that can be aligned with several different unit patterns.

    Whereas most programs focus on problem (1), problem (2) has - to my knowledge - only been solved in the
    Tandem Repeat Finder, which however uses a probabilistic, i.e. non-exact search algorithm.
    Phobos has been designed to solve problems (1) and (2).


    Development status:
    Phobos is still in development. However, since it is more accurate and more efficient than other
    search tools for tandem repeats that use an exact search algorithm, it has now been made available to the public.

    Currently, I am working on the following improvements:
    - a better filter for reporting alternative alignments
    - detection of compound satellites


    Phobos is in use since the end of 2006:
    - it has been used to detect tandem repeats in three genome projects now


    How to cite Phobos:
    Mayer, Christoph, Phobos 3.3.11, 2006-2010,
    <http://www.rub.de/spezzoo/cm/cm_phobos.htm>.

    If you are using the STAMP-module of the Staden-package, please also cite:
    Kraemer, L., Beszteri, B., Gaebler-Schwarz, S., Held, C., Leese, F., Mayer, C., Poehlmann, K. & Frickenhaus, S. (2009)
    STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
    BMC Bioinformatics 10:41.


    License:
    This program Phobos is copyright protected. It is only distributed from the authors web page.
    For academic and non-commercial usage this program can be used free of charge. Results obtained
    with this program can be published without restrictions, provided the program and its author are acknowledged by name.
    A commercial license for Phobos can be obtained from the author.


    Acknowledgements:
    I would like to thank the following collegues for helpful conversations and support:
    Florian Leese, AWI Bremerhaven
    Christoph Held, AWI Bremerhaven
    Bank Beszteri, AWI Bremerhaven
    Stephan Frickenhaus, AWI Bremerhaven



 
 
  Last update: September 2010, Christoph Mayer