Efficient Exact Pattern-Matching in Proteomic Sequences

Authors:
Sérgio Deusdado;Paulo Carvalho
Affiliations:
Department of Exact Sciences, ESA, Polytechnic Institute of Bragança, Portugal;Department of Informatics, Engineering School, University of Minho, Portugal
Venue:
IWANN '09 Proceedings of the 10th International Work-Conference on Artificial Neural Networks: Part II: Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living
Year:
2009

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Abstract

This paper proposes a novel algorithm for complete exact pattern-matching focusing the specificities of protein sequences (alphabet of 20 symbols) but, also highly efficient considering larger alphabets. The searching strategy uses large search windows allowing multiple alignments per iteration. A new filtering heuristic, named compatibility rule, contributed decisively to the efficiency improvement. The new algorithm's performance is, on average, superior in comparison with its best-rated competitors.