GIDT — A tool for the identification and visualization of genomic islands in prokaryotic organisms

Abstract

For decades, it has been a challenge for biologists to identify genomic islands (GIs) within a bacterial genome as they usually rapidly evolve. The purpose of this research is to develop an application which will analyse DNA sequences, enabling researchers to be up-to-date with bacterial evolution. A Java-based GI detection tool, “Genomic Islands Detection Tool (GIDT)" is introduced to detect GI regions by using a number of nucleotide-based statistical methods and genic methods (including GC-content variation, codon usage bias, dinucleotide frequency bias, tetranucleotide frequency bias, and k-mer signature analysis) and identification of mobility genes. It takes as input genome files in embl/genbank - file formats and returns probable GI regions in a tree-view display along with a circular-view display. GIDT is a simple tool which uses six GI identification algorithms and visually displays probable GI regions in a given genome. It runs on Microsoft windows, MacOS and Linux.