Bioinformatics Vol. 19 no. 3 2003
Pages 418-420
© 2003 Oxford University Press
Applications Note |
IslandPath: aiding detection of genomic islands in prokaryotes
1 Department of Molecular Biology and Biochemistry,
Simon Fraser University, Burnaby, BC, Canada V5A 1S6
2 Genome Sciences Centre, B.C. Cancer Agency,
Vancouver, BC, Canada V5Z 4E6
Received on September 4, 2002
; accepted on September 29, 2002
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{at}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.
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