Identification of weak motifs in multiple biological sequences using genetic algorithm

Authors:
Topon Kumar Paul;Hitoshi Iba
Affiliations:
The University of Tokyo, Kashiwa-shi Chiba, Japan;The University of Tokyo, Kashiwa-shi Chiba, Japan
Venue:
Proceedings of the 8th annual conference on Genetic and evolutionary computation
Year:
2006

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Abstract

Recognition of motifs in multiple unaligned sequences provides an insight into protein structure and function. The task of discovering these motifs is very challenging because most of these motifs exist in different sequences in different mutated forms of the original consensus motif and thus have weakly conserved regions. Different score metrics and algorithms have been proposed for motif recognition. In this paper, we propose a new genetic algorithm based method for identification of multiple motifs instances in multiple biological sequences. The experimental results on simulated and real data show that our algorithm can identify multiple occurrences of a weak motif in single sequences as well as in multiple sequences. Moreover, it can identify weakly conserved regions more accurately than other genetic algorithm based motif discovery methods.