Sequence Analysis Identification of compositionally distinct regions in genomes using

Motivation: It is known that most genomic regions of special inter-est, e.g., horizontally acquired sequences, genomic islands, etc., have distinct word (m-mer) compositions. Most of the earlier work along this direction, addressed di- and tri-nucleotide compositions. We present an approach that can be applied to analyze composi-tions of any given word size. The method, called the centroid ap-proach, can reveal compositionally distinct regions in genomic se-quences, for any given word size. Results: We applied our method to 50 bacterial genomes and demonstrated its ability to identify embedded sequences of varying lengths from distantly related organisms. We also investigated the genetic makeup of the regions identified as compositionally distinct by our method, for four organisms from our dataset. Pathogenicity island components and genes encoding strain-specific proteins are all frequently seen to be constituents of these regions. Availability: Program is available on request from the authors