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TitleEfficient exact pattern-matching in proteomic sequences
Author(s)Deusdado, Sérgio
Carvalho, Paulo
KeywordsExact pattern-matching
Searching algorithms
exact pattern-match
Issue dateJun-2009
JournalLecture Notes in Computer Science
CitationDeusdado S., Carvalho P. (2009) Efficient Exact Pattern-Matching in Proteomic Sequences. In: Omatu S. et al. (eds) Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living. IWANN 2009. Lecture Notes in Computer Science, vol 5518. Springer, Berlin, Heidelberg
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.
TypeConference paper
Publisher version
AccessOpen access
Appears in Collections:DI/CCTC - Artigos (papers)

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