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How to Multiply Dynamic Programming Algorithms

  • Christian Höner zu Siederdissen
  • Ivo L. Hofacker
  • Peter F. Stadler
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8213)

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/

Keywords

linear grammar context free grammar product structure multiple alignment Haskell 

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Copyright information

© Springer International Publishing Switzerland 2013

Authors and Affiliations

  • Christian Höner zu Siederdissen
    • 1
  • Ivo L. Hofacker
    • 1
    • 2
    • 3
  • Peter F. Stadler
    • 4
    • 1
    • 3
    • 5
    • 6
    • 7
  1. 1.Dept. Theoretical ChemistryUniv. ViennaWienAustria
  2. 2.Bioinformatics and Computational Biology Research GroupUniversity of ViennaViennaAustria
  3. 3.RTHUniv. CopenhagenDenmark
  4. 4.Dept. Computer Science, and Interdisciplinary Center for BioinformaticsUniv. LeipzigLeipzigGermany
  5. 5.MPI Mathematics in the SciencesLeipzigGermany
  6. 6.FHI Cell Therapy and ImmunologyLeipzigGermany
  7. 7.Santa Fe InstituteSanta FeUSA

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