IslandPath: aiding detection of genomic islands in prokaryotes

Genomic islands (clusters of genes of potential horizontal origin in a prokaryotic genome) are frequently associated with a particular adaptation of a microbe that is of medical, agricultural or environmental importance, such as antibiotic resistance, pathogen virulence, or metal resistance. While m...

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Bibliographic Details
Published in:Bioinformatics 2003-02, Vol.19 (3), p.418-420
Main Authors: Hsiao, William, Wan, Ivan, Jones, Steven J., Brinkman, Fiona S. L.
Format: Article
Language:English
Subjects:
Archaea - genetics
Bacteria - genetics
Biological and medical sciences
CpG Islands - genetics
Database Management Systems
Fundamental and applied biological sciences. Psychology
Gene Transfer, Horizontal
General aspects
Genome, Archaeal
Genome, Bacterial
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Phylogeny
Sequence Alignment - methods
Sequence Analysis, DNA - methods
Software
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Summary:Genomic islands (clusters of genes of potential horizontal origin in a prokaryotic genome) are frequently associated with a particular adaptation of a microbe that is of medical, agricultural or environmental importance, such as antibiotic resistance, pathogen virulence, or metal resistance. While many sequence features associated with such islands have been adopted separately in applications for analysis of genomic islands, including pathogenicity islands, there is no single application that integrates multiple features for island detection. IslandPath is a network service which incorporates multiple DNA signals and genome annotation features into a graphical display of a bacterial or archaeal genome, to aid the detection of genomic islands. Availability: This application is available at http://www.pathogenomics.sfu.ca/islandpath and the source code is freely available, under GNU public licence, from the authors. Contact: brinkman@sfu.ca Supplementary information: An online help file, which includes analyses of the utility of IslandPath, can be found at http://www.pathogenomics.sfu.ca/islandpath/current/islandhelp.html * To whom correspondence should be addressed.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btg004