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Calculating PSSM probabilities with lazy dynamic programming

Published online by Cambridge University Press:  13 September 2005

KETIL MALDE  and
ROBERT GIEGERICH
KETIL MALDE
Affiliation:
Department of Informatics, University of Bergen, Bergen, Norway (e-mail: ketil@ii.uib.no)
ROBERT GIEGERICH
Affiliation:
Faculty of Technology, University of Bielefeld, Bielefeld, Germany (e-mail: robert@techfak.uni-bielefeld.de)
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Abstract

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Position-specific scoring matrices are one way to represent approximate string patterns, which are commonly encountered in the field of bioinformatics. An important problem that arises with their application is calculating the statistical significance of matches. We review the currently most efficient algorithm for this task, and show how it can be implemented in Haskell, taking advantage of the built-in non-strictness of the language. The resulting program turns out to be an instance of dynamic programming, using lists rather the typical dynamic programming matrix.

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Type
Article
Information
Journal of Functional Programming , Volume 16 , Issue 1 , January 2006 , pp. 75 - 81
Copyright
© 2005 Cambridge University Press
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