Comparison of Genomes As 2-Level Pattern Analysis

Abstract:- This paper analyzes the gene pattern-location structures across related microbial genomes in an aim to extract their organizational and functional differences. We propose a sequence-ordered-set to represent the whole selected set of genes of a genome. The combined comparison of gene sequence similarity and relative location matching between genomes is then a 2-level pattern analysis, analogous to a comparison of random linear graph structure. Plots comparing between two genomes, depicting the highest similarity of each gene sequence from one genome to another for the whole set of genes were constructed. From the plot, additional analyses were performed using global rearrangement operations of: (1) shifts, (2) reversals, or (3) splits. Experiments were done using five closely related Chlamydia genomes that have substantial pathogenic differences. To analyze the relationship of pathogenic variation, the cell envelope set of genes was chosen. Results show consistent hierarchical gene rearrangements among genomes displaying similar pathogenicity. We hypothesize that an organizational structure may be intrinsic to the overall pathogenic functionality of these genomes. Results generally supported the hypothesis that genes of the cell envelope provide the variable loci required to form an effective source of variation among species that are otherwise very similar. Key-Words: linear random graph; Chlamydiae genome; cell envelope genes; organizational hierarchy; gene structure 1