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Erschienen in:
2009 | OriginalPaper | Buchkapitel
Efficient Exact Pattern-Matching in Proteomic Sequences
verfasst von : Sérgio Deusdado, Paulo Carvalho
Erschienen in: Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living
Verlag: Springer Berlin Heidelberg
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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.