Microbial genomic island discovery, visualization and analysis

IslandViewer update: improved genomic island discovery and visualization

IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a web-accessible application for the computational prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes. GIs are clusters of genes of probable horizontal origin and are of high interest because they disproportionately encode virulence factors and other adaptations of medical, environmental and industrial in...

IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis

IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a widely used web-based resource for the prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes. GIs are clusters of genes of probable horizontal origin, and are of high interest since they disproportionately encode genes involved in medically and environmentally important adaptations, including antimicrobial...

Distributed Visualization for Genomic Analysis

Neptune: A Tool for Rapid Microbial Genomic Signature Discovery

Neptune locates genomic signatures using an exact k -mer matching strategy while accommodating k -mer mismatches. The software identifies sequences that are sufficiently represented within “inclusion targets” and sufficiently absent from “exclusion targets”. The signature discovery process is accomplished using probabilistic models instead of heuristic strategies. We have evaluated Neptune on L...

Metagenomics: genomic analysis of microbial communities.

Uncultured microorganisms comprise the majority of the planet's biological diversity. Microorganisms represent two of the three domains of life and contain vast diversity that is the product of an estimated 3.8 billion years of evolution. In many environments, as many as 99% of the microorganisms cannot be cultured by standard techniques, and the uncultured fraction includes diverse organisms t...