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Bioinformatics Advance Access published online on January 16, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp030
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

IslandViewer: an integrated interface for computational identification and visualization of genomic islands

Morgan G. I. Langille and Fiona S. L. Brinkman *

Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada

*To whom correspondence should be addressed. Mr. Morgan Langille, E-mail: mlangill{at}sfu.ca, brinkman{at}sfu.ca


  Abstract

Summary: Genomic islands (clusters of genes of probable horizontal origin; GIs) play a critical role in medically important adaptations of bacteria. Recently, several computational methods have been developed to predict GIs that utilize either sequence composition bias or comparative genomics approaches. IslandViewer is a web accessible application that provides the first user-friendly interface for obtaining pre-computed GI predictions, or predictions from user-inputted sequence, using the most accurate methods for genomic island prediction: IslandPick, IslandPath-DIMOB, and SIGI-HMM. The graphical interface allows easy viewing and downloading of island data in multiple formats, at both the chromosome and gene level, for method-specific, or overlapping, GI predictions.

Availability: The IslandViewer web service is available at http://www.pathogenomics.sfu.ca/islandviewer and the source code is freely available under the GNU GPL license.

Contact: brinkman{at}sfu.ca

Associate Editor: Prof. Dmitrij Frishman

Received on October 18, 2008; revised on December 12, 2008; accepted on January 12, 2009

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