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Introduction to Stochastic Context Free Grammars

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RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1097))

Abstract

Stochastic context free grammars are a formalism which plays a prominent role in RNA secondary structure analysis. This chapter provides the theoretical background on stochastic context free grammars. We recall the general definitions and study the basic properties, virtues, and shortcomings of stochastic context free grammars. We then introduce two ways in which they are used in RNA secondary structure analysis, secondary structure prediction and RNA family modeling. This prepares for the discussion of applications of stochastic context free grammars in the chapters on Rfam (6), Pfold (8), and Infernal (9).

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Notes

  1. 1.

    Our definition is a bit more relaxed than the one found in the formal language literature.

  2. 2.

    Amusingly, the natural language processing community consistently refers to it as the CKY algorithm. The reason for such confusion is that there is no joint paper by these three authors. Reference [6] tells the story behind CYK. This classical textbook presents CYK because of its “intuitive simplicity,” but remains “doubtful, however, that it will find practical use.” Those were the days when a state-of-the-art computer had 65K bytes of memory.

  3. 3.

    When other types of scoring schemes are associated with G, such an efficiency improving transformation may not be possible. This has been called the yield parsing paradox in dynamic programming [7].

  4. 4.

    The present URL of this tool is http://www.brics.dk/grammar/.

References

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Acknowledgements

Thanks go to Jan Reinkensmeier for a careful reading of this manuscript.

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Authors and Affiliations

  1. Faculty of Technology and Center of Biotechnology, Bielefeld University, Bielefeld, Germany

    Robert Giegerich

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  1. Robert Giegerich
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Editors and Affiliations

  1. Center for non-coding RNA in Technology and Health, IKVH University of Copenhagen, Frederiksberg, Denmark

    Jan Gorodkin

  2. University of Washington Dept. Computer Science & Engineering, Seattle, Washington, USA

    Walter L. Ruzzo

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Giegerich, R. (2014). Introduction to Stochastic Context Free Grammars. In: Gorodkin, J., Ruzzo, W. (eds) RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Methods in Molecular Biology, vol 1097. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-709-9_5

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  • DOI: https://doi.org/10.1007/978-1-62703-709-9_5

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-708-2

  • Online ISBN: 978-1-62703-709-9

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