Open AccessDetecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis
Author(s) -
Tu Qiang,
Ding Dafu
Publication year - 2003
Publication title -
fems microbiology letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.899
H-Index - 151
eISSN - 1574-6968
pISSN - 0378-1097
DOI - 10.1016/s0378-1097(03)00204-0
Subject(s) - prophage , genome , pathogenicity island , gene , virulence , genetics , bacterial genome size , biology , bacterial adhesin , pathogenicity , computational biology , codon usage bias , bacteriophage , microbiology and biotechnology , escherichia coli
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.