A Novel Method for Reducing Computational Complexity of Whole Genome Sequence Alignment

National Institute of Advanced Industrial Science and Technology,Computational Biology Research Center,2-42 Aomi, Koto-ku, Tokyo 135-0064, JapanGenomic sequence alignment is a powerful tool for finding com mon subsequence patterns sharedby the input sequences and identifying evolutionary relationships between the species. However, therunning time and space requirement of genome alignment have often been very extensive. In thisresearch, we propose a novel algorithm called Coarse-Grained AlignmenT (CGAT) algorithm, forreducing computational complexity necessary for cross-species whole genome sequence alignment.The CGAT first divides the input sequences into ”blocks” with a fixed length and aligns these blocksto each other. The generated block-level alignment is then refined at the nucleotide level. This two-stepprocedure can drastically reduce the overall computational time and space necessary for an alignment.In this paper, we show the effectiveness of the proposed algorithm by applying it to whole genomesequences of several bacteria.Keywords: Genome Alignment; Multiple Alignment; Sequence Analysis; Comparative Genomics.