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

• Published in: Bioinformatics Vol. 25; no. 5; pp. 664 - 665
• Main Authors: Langille, Morgan G. I., Brinkman, Fiona S. L.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01-03-2009; Oxford Publishing Limited (England)
• Subjects: Applications Note; Bacteria; Biological and medical sciences; Computation; Computational Biology - methods; Computer Graphics; Format; Fundamental and applied biological sciences. Psychology; General aspects; Genes; Genomic Islands; Genomics - methods; Horizontal; Internet; Islands; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Software; Source code; User-Computer Interface; Viewing; Visualization; Identification; Genomics; Interface
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btp030

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 precomputed 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: [e-mail]