ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches.

ABSTRACT: There is a need for faster and more sensitive algorithms for sequence similarity searching in view of the rapidly increasing amounts of genomic sequence data available. Parallel processing capabilities in the form of the single instruction, multiple data (SIMD) technology are now available in common microprocessors and enable a single microprocessor to perform many operations in parallel. The ParAlign algorithm has been specifically designed to take advantage of this technology. The new algorithm initially exploits parallelism to perform a very rapid computation of the exact optimal ungapped alignment score for all diagonals in the alignment matrix. Then, a novel heuristic is employed to compute an approximate score of a gapped alignment by combining the scores of several diagonals. This a

SUBMITTER: Rognes T 

PROVIDER: S-EPMC31274 | biostudies-literature | 2001 Apr

REPOSITORIES: biostudies-literature