Finding submasses in weighted strings with Fast Fourier Transform

Authors:
Nikhil Bansal;Mark Cieliebak;Zsuzsanna Lipták
Affiliations:
IBM Research, T.J. Watson Research Center, New York, USA;Institute of Theoretical Computer Science, ETH Zurich, Switzerland and Center for Web Research, Department of Computer Science, University of Chile, Chile;AG Genome Informatics, Technical Faculty, University of Bielefeld, Postfach 10 01 31, D-33592 Bielefeld, Germany
Venue:
Discrete Applied Mathematics
Year:
2007

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Abstract

Position-specific score matrices (PSSMs) have been applied to various problems in computational molecular biology. In this paper, we study the following problem: given positive examples (sequences) and negative examples (sequences), find a PSSM which ...