Isfinder

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Text from the NAR 2007 Database Issue (Database Summaries) by permission of Oxford University Press.

Isfinder is NAR Database No. 832.

Contents

Database Description

ISfinder (http://www-is.biotoul.fr) is a dedicated database for bacterial Insertion Sequences (IS). It has superseded the Stanford reference center.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 IS sequences. 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 Insertion Sequences and transposons in general. On-line tools are gradually being added. At present an on-line BLAST facility against the entire bank is available. Additional features will include alignment capability, PSI-BLAST 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.

Authors

Siguier P.1, Perochon J.1, Lestrade L.1, Mahillon J.2 and Chandler M.1

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


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