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Bioniformatics is area, demanding knowledge and skills for acquisition, storing, management, analysis, interpretation and dissemination of biological information. This scientific area requires powerful computing resources for exploring large sets of biological data. Biological sequence processing is a key for molecular biology. Smith-Waterman algorithm, based on dynamic programming has become the most fundamental in bioinformatics. The goal of this paper is to investigate the efficiency of parallel multithreaded implementation based on Smith-Waterman algorithm. Performance parameters have been estimated by the experiments using various data sets on two parallel computer platforms.

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