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How to Multiply Dynamic Programming Algorithms

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Advances in Bioinformatics and Computational Biology (BSB 2013)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 8213))

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Abstract

We develop a theory of algebraic operations over linear grammars that makes it possible to combine simple “atomic” grammars operating on single sequences into complex, multi-dimensional grammars. We demonstrate the utility of this framework by constructing the search spaces of complex alignment problems on multiple input sequences explicitly as algebraic expressions of very simple 1-dimensional grammars. The compiler accompanying our theory makes it easy to experiment with the combination of multiple grammars and different operations. Composite grammars can be written out in \({\hbox{\LaTeX}}\) for documentation and as a guide to implementation of dynamic programming algorithms. An embedding in Haskell as a domain-specific language makes the theory directly accessible to writing and using grammar products without the detour of an external compiler. http://www.bioinf.uni-leipzig.de/Software/gramprod/

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Author information

Authors and Affiliations

  1. Dept. Theoretical Chemistry, Univ. Vienna, Währingerstr. 17, Wien, Austria

    Christian Höner zu Siederdissen, Ivo L. Hofacker & Peter F. Stadler

  2. Bioinformatics and Computational Biology Research Group, University of Vienna, 1090 Währingerstraße 17, Vienna, Austria

    Ivo L. Hofacker

  3. RTH, Univ. Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Denmark

    Ivo L. Hofacker & Peter F. Stadler

  4. Dept. Computer Science, and Interdisciplinary Center for Bioinformatics, Univ. Leipzig, Härtelstr. 16-18, Leipzig, Germany

    Peter F. Stadler

  5. MPI Mathematics in the Sciences, Inselstr. 22, Leipzig, Germany

    Peter F. Stadler

  6. FHI Cell Therapy and Immunology, Perlickstr. 1, Leipzig, Germany

    Peter F. Stadler

  7. Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, USA

    Peter F. Stadler

Authors
  1. Christian Höner zu Siederdissen
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  2. Ivo L. Hofacker
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  3. Peter F. Stadler
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Editor information

Editors and Affiliations

  1. Institute of Chemistry, University of São Paulo, Avenida Prof. Lineu Prestes, 748 sala 911, 05508-000, São Paulo, SP, Brazil

    João C. Setubal

  2. School of Computing, Facom-UFMS, Federal University of Mato Grosso do Sul, CP 549, Mato Grosso do Sul, 79070-900, MS, Brazil

    Nalvo F. Almeida

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Höner zu Siederdissen, C., Hofacker, I.L., Stadler, P.F. (2013). How to Multiply Dynamic Programming Algorithms. In: Setubal, J.C., Almeida, N.F. (eds) Advances in Bioinformatics and Computational Biology. BSB 2013. Lecture Notes in Computer Science(), vol 8213. Springer, Cham. https://doi.org/10.1007/978-3-319-02624-4_8

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  • DOI: https://doi.org/10.1007/978-3-319-02624-4_8

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-02623-7

  • Online ISBN: 978-3-319-02624-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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