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Nucleic Acids Research Advance Access published online on November 11, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp947
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

ISbrowser: an extension of ISfinder for visualizing insertion sequences in prokaryotic genomes

Pryavahiny Kichenaradja, Patricia Siguier, Jocelyne Pérochon and Michael Chandler*

Laboratoire de Microbiologie et Génétique Moléculaires, C.N.R.S.,118 Route de Narbonne, F-31062 Toulouse Cedex, France

*To whom correspondence should be addressed. Tel: +335 61 33 58 58; Fax: +335 61 33 58 61; Email: mike{at}ibcg.biotoul.fr

Received September 14, 2009. Revised October 9, 2009. Accepted October 12, 2009.

Insertion sequences (ISs) are among the smallest and simplest autonomous transposable elements. ISfinder (http://www-is.biotoul.fr/) is a dedicated IS database which assigns names to individual ISs to maintain a coherent nomenclature, an IS repository including >3000 individual ISs from both bacteria and archaea and provides a basis for IS classification. Each IS is indexed in ISfinder with various associated pieces of information (the complete nucleotide sequence, the sequence of the ends and target sites, potential open reading frames, strain of origin, distribution in other strains and available bibliography) and classified into a group or family to provide some insight into its phylogeny. ISfinder also includes extensive background information on ISs and transposons in general. Online tools are gradually being added. At present, it is difficult to visualize the global distribution of ISs in a given bacterial genome. Such information would facilitate understanding of the impact of these small transposable elements on shaping their host genome. Here we describe ISbrowser (http://www-genome.biotoul.fr/ISbrowser.php), an extension to the ISfinder platform and a tool which permits visualization of the position, orientation and distribution of complete and partial ISs in individual prokaryotic genomes.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors'


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