Utilize este identificador para referenciar este registo: http://hdl.handle.net/10198/2259
Título: GRASPm: an efficient algorithm for exact pattern-matching in genomic sequences
Autor: Deusdado, Sérgio
Carvalho, Paulo
Palavras-chave: Pattern-matching
Sequence searching and analisys
Motif discovery
Data: 2009
Editora: Inderscience Publishers
Citação: International Journal of Bioinformatics Research and Applications. ISSN 1744-5485. 5:4 (2009) p. 385-401
Resumo: In this paper, we propose Genomic-oriented Rapid Algorithm for String Pattern-match (GRASPm), an algorithm centred on overlapped 2-grams analysis, which introduces a novel filtering heuristic – the compatibility rule – achieving significant efficiency gain. GRASPm’s foundations rely especially on a wide searching window having the central duplet as reference for fast filtering of multiple alignments. Subsequently, superfluous detailed verifications are summarily avoided by filtering the incompatible alignments using the idcd (involving duplet of central duplet) concept combined with pre-processed conditions, allowing fast parallel testing for multiple alignments. Comparative performance analysis, using diverse genomic data, shows that GRASPm is faster than its competitors.
URI: http://hdl.handle.net/10198/2259
ISSN: 1744-5485
Versão do Editor: http://inderscience.metapress.com/link.asp?id=t213508542710676
Aparece nas colecções:CSE - Artigos em Revistas Indexados no ISI/Scopus

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