A fast fuzzy Cocke-Younger-Kasami algorithm for DNA and RNA strings analysis

Authors:
Herón Molina-Lozano
Affiliations:
Centro de Investigación en Computación, Instituto Politécnico Nacional, México D.F.
Venue:
MICAI'10 Proceedings of the 9th Mexican international conference on Artificial intelligence conference on Advances in soft computing: Part II
Year:
2010

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Abstract

In this paper we present a variation of the Cocke-Younger-Kasami algorithm (CYK algorithm for short) for the analysis of fuzzy free context languages applied to DNA strings. We propose a variation of the original CYK algorithm where we prove that the order of the new CYK algorithm is O(n). We prove that the new algorithm only use 2n-1 memory localities. We use a variation of the CYK algorithm, where the free context language can be fuzzy. The fuzzy context-free grammar (FCFG) is obtained from DNA and RNA sequences.