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Authors
Advisor(s)
Abstract(s)
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.
Description
Keywords
Exact pattern-match Searching algorithms
Citation
Deusdado, Sérgio; Carvalho, Paulo (2009). Efficient exact pattern-matching in proteomic sequences. In Omatu, Sigeru [et al.] Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living. Berlin: Springer-Verlag. p. 1178-1186. ISBN 978-3-642-02480-1