Evaluation of genomic island predictors using a comparative genomics approach

Background: Genomic islands (GIs) are clusters of genes in prokaryotic genomes of probable horizontal origin. GIs are disproportionately associated with microbial adaptations of medical or environmental interest. Recently, multiple programs for automated detection of GIs have been developed that utilize sequence composition characteristics, such as G+C ratio and dinucleotide bias. To robustly evaluate the accuracy of such methods, we propose that a dataset of GIs be constructed using criteria that are independent of sequence composition-based analysis approaches. Results: We developed a comparative genomics approach (IslandPick) that identifies both very probable islands and non-island regions. The approach involves 1) flexible, automated selection of comparative genomes for each query genome, using a distance function that picks appropriate genomes for identification of GIs, 2) identification of regions unique to the query genome, compared with the chosen genomes (positive dataset) a...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Morgan G. I. Langille, William W. L. Hsiao, Fiona S. L. Brinkman
• Keywords: BMCBI 2008, Genomes, Query Genome, Sequence Composition-based Gi