title: Strain-specific genes of Helicobacter pylori: distribution, function and dynamics.
abstract: Whole-genome clustering of the two available genome sequences of Helicobacter pylori strains 26695 and J99 allows the detection of 110 and 52 strain-specific genes, respectively. This set of strain-specific genes was compared with the sets obtained with other computational approaches of direct genome comparison as well as experimental data from microarray analysis. A considerable number of novel function assignments is possible using database-driven sequence annotation, although the function of the majority of the identified genes remains unknown. Using whole-genome clustering, it is also possible to detect species-specific genes by comparing the two H.pylori strains against the genome sequence of Campylobacter jejuni. It is interesting that the majority of strain-specific genes appear to be species specific. Finally, we introduce a novel approach to gene position analysis by employing measures from directional statistics. We show that although the two strains exhibit differences with respect to strain-specific gene distributions, this is due to the extensive genome rearrangements. If these are taken into account, a common pattern for the genome dynamics of the two Helicobacter strains emerges, suggestive of certain spatial constraints that may act as control mechanisms of gene flux.
authors.affiliation: Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.
authors.forename: P J
authors.initials: PJ
authors.lastname: Janssen
authors.forename: B
authors.initials: B
authors.lastname: Audit
authors.forename: C A
authors.initials: CA
authors.lastname: Ouzounis
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics / Q000378:metabolism; D016123:Campylobacter jejuni / Q000235:genetics; D019295:Computational Biology; D030562:Databases, Protein; D019143:Evolution, Molecular; D023061:Gene Order / Q000235:genetics; D005798:Genes, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D023281:Genomics; D016480:Helicobacter pylori / Q000145:classification* / Q000235:genetics*; D020407:Internet; D008957:Models, Genetic; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D013045:Species Specificity
chemical_list: D001426:Bacterial Proteins