Efficient Algorithms for Local Alignment Search

S. Rajasekaran, H. Nick, P.M. Pardalos, S. Sahni and G. Shaw
Additional contact information
S. Rajasekaran: University of Florida
H. Nick: University of Florida
P.M. Pardalos: University of Florida
S. Sahni: University of Florida
G. Shaw: University of Florida

Journal of Combinatorial Optimization, 2001, vol. 5, issue 1, No 8, 117-124

Abstract: Abstract We present efficient algorithms for local alignment search in biological sequences. These algorithms identify maximal segment pairs (MSPs). Our algorithms have the potential of performing better than BLAST (Basic Local Alignment Search Tool) and also are efficiently parallelizable. We employ Fast Fourier Transforms (FFTs). Though several attempts have been made in the past to employ FFTs in sequence analysis, they fail to capture local similarities. Our algorithms employ FFTs in a novel way to identify local similarities. FFT-based techniques have the attractive feature of benefiting from ultrafast special purpose hardware available for digital signal processing.

Keywords: local alignment research; BLAST; biological sequences; DNA sequences; protein sequences; parallel computing (search for similar items in EconPapers)
Date: 2001
References: View complete reference list from CitEc
Citations: View citations in EconPapers (1)

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DOI: 10.1023/A:1009893719470

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