title: Prediction of genomic islands in three bacterial pathogens of pneumonia.
abstract: Pneumonia is one kind of common infectious disease, which is usually caused by bacteria, viruses, or fungi. In this paper, we predicted genomic islands in three bacterial pathogens of pneumonia. They are Chlamydophila pneumoniae, Mycoplasma pneumoniae and Streptococcus pneumoniae, respectively. For each pathogen, one clinical strain is involved. After implementing the cumulative GC profile combined with h and BCN index, eight genomic islands are found in three pathogens. Among them, six genomic islands are found to have mobility elements, which constitute a kind of conserved character of genomic islands, and this introduces the possibility that they are genuine genomic islands. The present results show that the cumulative GC profile when combined with h and BCN indexes is a good method for predicting genomic islands in bacteria and it has lower false positive rate than the SIGI method. Specially, three genomic islands are found to contain clusters of genes coding for production of virulence factors and this is useful for research into the pathogenicity of these pathogens and helpful for the treatment of diseases caused by them.
authors.affiliation: Center of Bioinformatics and Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors.forename: Feng-Biao
authors.initials: FB
authors.lastname: Guo
authors.affiliation: Center of Bioinformatics and Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors.forename: Wen
authors.initials: W
authors.lastname: Wei
mesh_terms: D001482:Base Composition; D061387:Chlamydial Pneumonia / Q000382:microbiology; D016993:Chlamydophila pneumoniae / Q000235:genetics / Q000472:pathogenicity; D004269:DNA, Bacterial / Q000235:genetics; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D044404:Genomic Islands; D006801:Humans; D009177:Mycoplasma pneumoniae / Q000235:genetics / Q000472:pathogenicity; D018410:Pneumonia, Bacterial / Q000382:microbiology*; D011019:Pneumonia, Mycoplasma / Q000382:microbiology; D011018:Pneumonia, Pneumococcal / Q000382:microbiology; D013296:Streptococcus pneumoniae / Q000235:genetics / Q000472:pathogenicity
chemical_list: D004269:DNA, Bacterial