Table of Contents
International Scholarly Research Notices
Volume 2014, Article ID 732857, 9 pages
http://dx.doi.org/10.1155/2014/732857
Research Article

A Computational Framework for Tracing the Origins of Genomic Islands in Prokaryotes

Department of Computer Science, East Stroudsburg University, 200 Prospect Street, East Stroudsburg, PA 18301, USA

Received 6 June 2014; Revised 27 July 2014; Accepted 30 July 2014; Published 28 October 2014

Academic Editor: Yudong Cai

Copyright © 2014 Peng Wan and Dongsheng Che. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Genomic islands (GIs) are chunks of genomic fragments that are acquired from nongenealogical organisms through horizontal gene transfer (HGT). Current researches on studying donor-recipient relationships for HGT are limited at a gene level. As more GIs have been identified and verified, the way of studying donor-recipient relationships can be better modeled by using GIs rather than individual genes. In this paper, we report the development of a computational framework for detecting origins of GIs. The main idea of our computational framework is to identify GIs in a query genome, search candidate genomes that contain genomic regions similar to those GIs in the query genome by BLAST search, and then filter out some candidate genomes if those similar genomic regions are also alien (detected by GI detection tools). We have applied our framework in finding the GI origins for Mycobacterium tuberculosis H37Rv, Herminiimonas arsenicoxydans, and three Thermoanaerobacter species. The predicted results were used to establish the donor-recipient network relationships and visualized by Gephi. Our studies have shown that donor genomes detected by our computational approach were mainly consistent with previous studies. Our framework was implemented with Perl and executed on Windows operating system.