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Efficient Algorithms for Local Alignment Search |
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| Authors: | S. Rajasekaran H. Nick P.M. Pardalos S. Sahni G. Shaw |
| Affiliation: | (1) Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611-9083, USA;(2) Department of Neuroscience, University of Florida, Gainesville, FL 32611-9083, USA;(3) Department of Industrial Systems Engineering, University of Florida, Gainesville, FL 32611-9083, USA |
| 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 |
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