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

By M. Langille, Fiona S. L. Brinkman. Bioinform., 2009

412 citations recorded by the source corpus.

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. Contact: brinkman@sfu.ca

Subfields: Food Science, Genetics

View Paper: https://www.semanticscholar.org/paper/af73f2a2bccb0d79f4f6c01d0a8f8b8ca1f4ef8a

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Citations in the corpus

Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes (2010, methodology): “Views of the data in IslandViewer have been integrated into the Pseudomonas Genome Database from a ‘browse genomic island’ page and from individual strain summary pages.”
IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets (2017, neutral): “Initially published in 2009 (15), IslandViewer was the first webserver integrating three of the most accurate and complementary GI prediction tools; IslandPath-DIMOB (16) based on nucleotide bias and presence of mobility genes, SIGI-HMM (17) based on codon usage bias with a Hidden Markov Model appro”
CRISPRTarget (2013, background): “Spacer 3 in CRISPR4 matches a transposase gene in Pectobacterium wasabiae WPP163 (Pecwa_0911), which is not predicted to be part of an island.(70) P.”
Ecology of marine Bacteroidetes: a comparative genomics approach (2013, methodology): “Genomic islands (GIs) of Polaribacter sp. MED152, Dokdonia sp. MED134, L. blandensis MED217 and ‘G. forsetii’ KT0803 were extracted (Fernández-Gómez et al., 2012) using IslandViewer database for identification and visualization of GIs (Langille and Brinkman, 2009; Langille et al., 2010).”