Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis.
We present a simple method to detect pathogenicity islands and anomalous gene clusters in bacterial genomes. The method uses iterative discriminant analysis to define genomic regions that deviate most from the rest of the genome in three compositional criteria: G+C content, dinucleotide frequency and codon usage. Using this method, we identify many virulence-related gene islands, e.g. encoding protein secretion systems, adhesins, toxins, and other anomalous gene clusters, such as prophages. The program and the whole dataset, including the catalogs of genes in the detected anomalous segments, are publicly available at http://compbio.sibsnet.org/projects/pai-ida/. This program can be used in searching for virulence-related factors in newly sequenced bacterial genomes.
Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China. tuqiang@mail.shcnc.ac.cn
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D000465:Algorithms; D001419:Bacteria / Q000235:genetics / Q000472:pathogenicity*; D004269:DNA, Bacterial; D016680:Genome, Bacterial; D005810:Multigene Family; D017422:Sequence Analysis, DNA
D004269:DNA, Bacterial