PLUMMER: An Almost Linear Approach to Multiple Whole Genome Alignment

Following advances in biotechnology, many new whole genome sequences are becom- ing available every year. A lot of useful information can be derived from the alignment and comparison of different genomes. However, most of the current research focuses on pairwise genome alignment, and few available applications can efciently align multiple genomes. In this paper, we present an optimal approach to multiple whole genome alignment. Our algo- rithm aligns closely related multiple genomes to nd their conserved regions. We present two approaches to align whole genomes. In rst approach, called Direct Matching (DM), multi- ple whole genomes are aligned with their DNA sequences. However, because most parts of prokaryotic genomes are encoded regions, we introduce second method, Functional Matching (FM), to especially align multiple prokaryotic genomes. We present graph theoretic argu- mentation to prove that our approach has almost linear complexity. In addition, analyses of experimental results for both methods are presented. It may be noted that the FM method gen- erates a greater number of and longer conserved regions than the DM method and thus conveys detailed and accurate information about the conservation and inheritance of genomes.