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Related Experiment Video

Updated: Jan 2, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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AgdbNet - antigen sequence database software for bacterial typing.

Keith A Jolley1, Martin C J Maiden

  • 1The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK. keith.jolley@medawar.ox.ac.uk

BMC Bioinformatics
|June 23, 2006
PubMed
Summary
This summary is machine-generated.

agdbNet software enables rapid creation of customized internet antigen sequence databases for bacterial typing. This tool facilitates simultaneous BLAST querying across multiple gene loci, supporting diverse typing schemes.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Computational Biology

Background:

  • Bacterial typing schemes rely on antigen gene sequences and require standardized nomenclature databases.
  • Developing these databases often necessitates custom coding for web integration.
  • Existing methods face challenges due to diverse gene targets and typing scheme variations.

Purpose of the Study:

  • To introduce agdbNet, a versatile web database software for bacterial antigen sequence analysis.
  • To provide a solution for creating uniform, curated, and accessible nomenclature databases.
  • To facilitate simultaneous querying of multiple genetic loci using sequence data.

Main Methods:

  • agdbNet utilizes XML files to describe databases, parsed by a Perl CGI script.
  • Databases can incorporate multiple loci defined by nucleotide and/or peptide sequences.
  • The software supports simultaneous BLAST querying of nucleotide or peptide sequences across multiple loci.

Main Results:

  • agdbNet is currently used in five public databases for typing Neisseria meningitidis, Campylobacter jejuni, and Streptococcus equi.
  • The software can query internal isolate tables or external databases like those for multilocus sequence typing.
  • Website appearance is fully configurable via stylesheets and custom header/footer files.

Conclusions:

  • agdbNet offers a fast method for establishing customized internet antigen sequence databases.
  • Flexible configuration options accommodate typing schemes with diverse requirements.
  • The software standardizes bacterial variant nomenclature for improved data sharing and analysis.