GRASPm: An efficient algorithm for exact pattern-matching in genomic sequences

Sérgio Deusdado¹, Paulo Carvalho²

Instituto Politécnico de Bragança¹
P-5300 Bragança, Portugal
E-mail: sergiod at ipb.pt

Universidade do Minho²
Departamento de Informática
P-4710-057 Braga, Portugal

E-mail: pmc at di.uminho.pt

Abstract 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.

in International Journal of Bioinformatics Research and Applications, InderScience Publishers, vol.5, n.4, 2009