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Bioinformatics. 2009 Mar 1;25(5):664-5. doi: 10.1093/bioinformatics/btp030. Epub 2009 Jan 16.

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

Author information

  • 1Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.

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 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.

PMID:
19151094
[PubMed - indexed for MEDLINE]
PMCID:
PMC2647836
Free PMC Article
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