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Related Experiment Videos

ACLAME: a CLAssification of Mobile genetic Elements.

Raphaël Leplae1, Aline Hebrant, Shoshana J Wodak

  • 1Service de Conformation de Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles, Belgium. raphael@scmbb.ulb.ac.be

Nucleic Acids Research
|December 19, 2003
PubMed
Summary

The ACLAME database classifies prokaryotic mobile genetic elements (MGEs) like phages and plasmids. It uses automated and manual methods to organize MGE protein functions, improving genomic annotation.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Prokaryotic mobile genetic elements (MGEs) are crucial for bacterial evolution and adaptation.
  • Existing databases lack comprehensive functional classification of MGEs, hindering research.
  • Accurate annotation of MGEs is essential for understanding genome dynamics.

Purpose of the Study:

  • To establish the ACLAME database, a curated collection and classification of prokaryotic MGEs.
  • To provide a functional classification of MGE proteins, genes, and modules.
  • To improve the annotation of MGEs and facilitate the discovery of new MGEs.

Main Methods:

  • Collected and classified prokaryotic MGEs, including phage genomes, plasmids, and transposons.
  • Employed TRIBE-MCL, a graph-theory-based clustering algorithm, for automated protein classification.

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  • Performed manual curation using Psi-Blast and Hidden Markov Models for enhanced accuracy.

    • Main Results:

    • Developed ACLAME, classifying 5069 proteins from 119 DNA bacteriophages into over 400 functional families.
    • Integrated comprehensive MGE data, including full genomes and genetic entities.
    • Established a publicly accessible database with browsing and querying capabilities.

    Conclusions:

    • ACLAME offers a rational organization of MGE complexity and improved functional annotation.
    • The database serves as a valuable resource for MGE research and discovery.
    • Encourages expert volunteer participation to enhance ongoing curation efforts.