Efficient algorithms for local alignment search

We present efficient algorithms for local alignment search in biological se quences. These algorithms identify maximal segment pairs (MSPs). Our algori thms have the potential of performing better than BLAST (Basic Local Alignm ent Search Tool) and also are efficiently parallelizable. We employ Fast Fo urier Transforms (FFTs). Though several attempts have been made in the past to employ FFTs in sequence analysis, they fail to capture local similariti es. Our algorithms employ FFTs in a novel way to identify local similaritie s. FFT-based techniques have the attractive feature of benefiting from ultr afast special purpose hardware available for digital signal processing.