Paralellization of Needleman-Wunsch String Alignment Method

The identification of homologies between protein sequences is a central problem in molecular biology and several algorithms have been proposed for accomplishing this task. The Needleman-Wunsch Algorithm and its close variant, the SmithWaterman dynamic programming methods, solve the problem exactly in quadratic time and space. However, due to the massive amount of data involved in sequence-to-database of sequences comparisons, heuristic methods such as BLAST, are used instead. This article explores the design of a parallel version of Needleman-Wunsch based on a divide-and-conquer idea derived from an algorithm first proposed by Hirschberg, for the identification of the longest common substring of two strings.