title: A computational tool for the genomic identification of regions of unusual compositional properties and its utilization in the detection of horizontally transferred sequences.
abstract: Similarity Plot (S-plot) is a Windows-based application for large-scale comparisons and 2-dimensional visualization of compositional similarities between genomic sequences. This application combines 2 approaches widely used in genomics: window analysis of statistical characteristics along genomes and dot-plot visual representation. S-plot is effective in identifying highly similar regions between genomes as well as regions with unusual compositional properties (RUCPs) within a single genome, which may be indicative of horizontal gene transfer or of locus-specific selective forces. We use S-plot to identify regions that may have originated through horizontal gene transfer through a 2-step approach, by first comparing a genomic sequence to itself and, subsequently, comparing it to the genomic sequence of a closely related taxon. Moreover, by comparing these suspect sequences to one another, we can estimate a minimum number of sources for these putative xenologous sequences. We illustrate the uses of S-plot in a comparison involving Escherichia coli K12 and E. coli O157:H7. In O157:H7, we found 145 regions that have most probably originated through horizontal gene transfer. By using S-plot to compare each of these regions with 277 completely sequenced prokaryotic genomes, 1 sequence was found to have similar compositional properties to the Yersinia pseudotuberculosis genome, indicating a transfer from a Yersinia or Yersinia relative. Based upon our analysis of RUCPs in O157:H7, we infer that there were at least 53 sources of horizontally transferred sequences.
authors.affiliation: Department of Computer Science, University of Houston, USA.
authors.forename: Catherine
authors.initials: C
authors.lastname: Putonti
authors.forename: Yi
authors.initials: Y
authors.lastname: Luo
authors.forename: Charles
authors.initials: C
authors.lastname: Katili
authors.forename: Sergey
authors.initials: S
authors.lastname: Chumakov
authors.forename: George E
authors.initials: GE
authors.lastname: Fox
authors.forename: Dan
authors.initials: D
authors.lastname: Graur
authors.forename: Yuriy
authors.initials: Y
authors.lastname: Fofanov
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics; D048168:Escherichia coli K12 / Q000235:genetics; D019453:Escherichia coli O157 / Q000235:genetics; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D023281:Genomics / Q000706:statistics & numerical data*; D012984:Software; D013045:Species Specificity; D015011:Yersinia pseudotuberculosis / Q000235:genetics
chemical_list: D004269:DNA, Bacterial