High Performance Multiple Sequence Alignment Algorithms for Comparison of Microbial Genomes

Abstract

Advances in gene sequencing have enabled in silico analyses of microbial genomes and have led to the revision of concepts of microbial taxonomy and evolution. We explore deficiencies in existing multiple sequence global alignment algorithms and introduce a new indexing scheme to partition the dynamic programming algorithm hypercube scoring tensor over processors based on the dependency between partitions to be scored in parallel. The performance of algorithms is compared in the study of rpoB gene sequences of Mycoplasma species.