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Nucleic Acids Research 2006 34(Database Issue):D32-D36; doi:10.1093/nar/gkj014
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Nucleic Acids Research, 2006, Vol. 34, Database issue D32-D36
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

ISfinder: the reference centre for bacterial insertion sequences

P. Siguier, J. Perochon, L. Lestrade, J. Mahillon1 and M. Chandler*

Laboratoire de Microbiologie et Génétique Moléculaires, C.N.R.S. 118 Route de Narbonne, F-31062 Toulouse Cedex, France 1Laboratoire de Microbiologie Alimentaire et Environnementale, Université catholique de Louvain Croix du Sud, 2 Bte 12, B-1348 Louvain-la-Neuve, Belgium

*To whom correspondence should be addressed. Tel: +33 5 61 33 58 58; Fax: +33 5 61 33 58 86; Email: mike{at}ibcg.biotoul.fr

Received August 11, 2005. Revised September 14, 2005. Accepted September 14, 2005.

ISfinder (www-is.biotoul.fr) is a dedicated database for bacterial insertion sequences (ISs). It has superseded the Stanford reference center. One of its functions is to assign IS names and to provide a focal point for a coherent nomenclature. It is also the repository for ISs. Each new IS is indexed together with information such as its DNA sequence and open reading frames or potential coding sequences, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography where available. Another objective is to continuously monitor ISs to provide updated comprehensive groupings or families and to provide some insight into their phylogenies. The site also contains extensive background information on ISs and transposons in general. Online tools are gradually being added. At present an online Blast facility against the entire bank is available. But additional features will include alignment capability, PsiBLAST and HMM profiles. ISfinder also includes a section on bacterial genomes and is involved in annotating the IS content of these genomes. Finally, this database is currently recommended by several microbiology journals for registration of new IS elements before their publication.


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