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ISfinder: the reference centre for bacterial insertion sequences.

P Siguier1, J Perochon, L Lestrade

  • 1Laboratoire de Microbiologie et Génétique Moléculaires, C.N.R.S. 118, Route de Narbonne, F-31062 Toulouse Cedex, France.

Nucleic Acids Research
|December 31, 2005
PubMed
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ISfinder is a comprehensive bacterial insertion sequence (IS) database, offering naming, data submission, and phylogenetic analysis. It serves as a central repository and recommended platform for IS registration in microbiology.

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Bacterial insertion sequences (ISs) are mobile genetic elements with significant roles in genome evolution.
  • A centralized, standardized resource is crucial for managing and understanding IS diversity and activity.
  • The Stanford reference center was previously a key resource, but ISfinder has now superseded it.

Purpose of the Study:

  • To introduce ISfinder as a dedicated, comprehensive database for bacterial insertion sequences.
  • To highlight ISfinder's functionalities in IS nomenclature, data archiving, and phylogenetic analysis.
  • To emphasize ISfinder's role in annotating IS content within bacterial genomes and its recommendation by journals.

Main Methods:

  • ISfinder integrates DNA sequences, open reading frames, element ends, and target site data.

Related Experiment Videos

  • It provides tools for monitoring ISs, updating classifications into families, and inferring phylogenies.
  • The database includes background information on ISs and transposons, with plans for additional online tools like BLAST, alignment, PsiBLAST, and HMM profiles.

    • Main Results:

    • ISfinder serves as a central repository and focal point for coherent IS nomenclature.
    • It archives detailed information for each new IS, including sequence data, origin, and distribution.
    • The database facilitates the continuous monitoring and updated classification of IS elements.

    Conclusions:

    • ISfinder is an essential, up-to-date resource for bacterial insertion sequences, supporting research and nomenclature.
    • Its comprehensive data and analytical tools aid in understanding IS evolution and genomic impact.
    • ISfinder is the recommended platform for the registration of novel IS elements prior to publication.