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Authors
Advisor(s)
Abstract(s)
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.
Description
Keywords
Pattern-matching Sequence searching and analisys Motif discovery
Citation
International Journal of Bioinformatics Research and Applications. ISSN 1744-5485. 5:4 (2009) p. 385-401
Publisher
Inderscience Publishers