A computational approach for identifying pathogenicity islands in prokaryotic genomes

Background: Pathogenicity islands (PAIs), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (GIs) that have been acquired by horizontal gene transfer event. Up to now, computational approaches for identifying PAIs have been focused on the detection of genomic regions which only differ from the rest of the genome in their base composition and codon usage. These approaches often lead to the identification of genomic islands, rather than PAIs. Results: We present a computational method for detecting potential PAIs in complete prokaryotic genomes by combining sequence similarities and abnormalities in genomic composition. We first collected 207 GenBank accessions containing either part or all of the reported PAI loci. In sequenced genomes, strips of PAI-homologs were defined based on the proximity of the homologs of genes in the same PAI accession. An algorithm reminiscent of sequence-assembly procedure was then devised to merge ove...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Sung Ho Yoon, Cheol-Goo Hur, Ho-Young Kang, Yeoun Hee Kim, Tae Kwang Oh, Jihyun F. Kim
• Keywords: BMCBI 2005, Genomic, Genomic Regions, PAIs