title: Detecting genomic islands using bioinformatics approaches.
abstract: Bacterial genomes contain clusters of genes that are acquired by horizontal transfer, called genomic islands (GIs). GIs are frequently associated with microbial adaptations that are of medical and environmental interest, and they have had a substantial impact on bacterial evolution. Therefore, there is growing interest in efficiently identifying GIs in newly sequenced bacterial genomes. Several computational methods for detecting GIs have been developed recently, presenting researchers with a myriad of choices. Here, we discuss the limitations and benefits of the main approaches that are available and present guidelines to aid researchers in effectively identifying these important genomic regions.
authors.affiliation: UC Davis Genome Center, University of California, Davis, One Shields Avenue, Davis, California 95616, USA.
authors.forename: Morgan G I
authors.initials: MG
authors.lastname: Langille
authors.forename: William W L
authors.initials: WW
authors.lastname: Hsiao
authors.forename: Fiona S L
authors.initials: FS
authors.lastname: Brinkman
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000472:pathogenicity; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D016680:Genome, Bacterial; D044404:Genomic Islands; D023281:Genomics / Q000379:methods / Q000706:statistics & numerical data; D014774:Virulence / Q000235:genetics
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