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BAGEL: a web-based bacteriocin genome mining tool.

Anne de Jong1, Sacha A F T van Hijum, Jetta J E Bijlsma

  • 1Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands.

Nucleic Acids Research
|July 18, 2006
PubMed
Summary

BAGEL is a new web server that identifies bacteriocin genes, which are often missed in genome annotations. It uses novel databases and genomic context to find these important antimicrobial peptide genes.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Identifying functionally similar genes with low sequence homology is challenging.
  • Bacteriocins, diverse antimicrobial peptides, are often encoded by small, poorly conserved open reading frames (ORFs) missed during genome annotation.
  • Surrounding ORFs often encode biosynthetic genes, offering clues to locate bacteriocin genes.

Purpose of the Study:

  • To develop a web server, BAGEL, for identifying putative bacteriocin ORFs in DNA sequences.
  • To improve the detection of bacteriocin genes, especially those missed in standard annotation processes.
  • To leverage genomic context for more accurate bacteriocin gene cluster identification.

Main Methods:

  • Utilized novel, knowledge-based bacteriocin and motif databases.

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  • Implemented ORF detection using multiple published ORF prediction tools.
  • Analyzed genomic context of potential bacteriocin-encoding ORFs for associated biosynthesis, transport, regulation, and immunity genes.

    • Main Results:

    • BAGEL successfully identifies putative bacteriocin ORFs.
    • The tool accounts for small, conserved gene features often overlooked in genome annotation.
    • BAGEL can detect putative bacteriocin gene clusters within bacterial genomes by analyzing genomic context.

    Conclusions:

    • BAGEL offers a unique approach to discover bacteriocin gene clusters in bacterial genomes.
    • The web server enhances the annotation of bacterial genomes by identifying previously missed bacteriocin genes.
    • BAGEL is a valuable tool for bacteriocin research and antimicrobial discovery.