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Related Experiment Videos

Towards pathogenomics: a web-based resource for pathogenicity islands.

Sung Ho Yoon1, Young-Kyu Park, Soohyun Lee

  • 1Systems Microbiology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 52 Oun-dong, Yuseong, Daejeon 305-806, Republic of Korea.

Nucleic Acids Research
|November 9, 2006
PubMed
Summary

Pathogenicity islands (PAIs) are crucial genetic elements in disease development. A new database, PAIDB, aids in identifying these horizontally transferred elements in pathogenic bacteria, advancing pathogenomics research.

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Pathogenicity islands (PAIs) are mobile genetic elements facilitating microbial pathogenesis.
  • Horizontal gene transfer of PAIs significantly contributes to the evolution of bacterial virulence.
  • Understanding PAI distribution is key to deciphering microbial disease mechanisms.

Purpose of the Study:

  • To establish a comprehensive database (PAIDB) for pathogenicity islands.
  • To develop specialized search tools for PAI identification.
  • To facilitate research in pathogenomics by providing a user-friendly resource.

Main Methods:

  • Developed a relational database integrating reported and predicted PAIs.
  • Employed a combined feature-based and similarity-based analysis for PAI prediction.

Related Experiment Videos

  • Created the PAI Finder search application for onsite multi-sequence queries.

    • Main Results:

    • PAIDB contains 112 PAI types and 889 GenBank accessions across 497 pathogenic bacterial strains.
    • Identified 310 candidate PAIs from 118 sequenced prokaryotic genomes.
    • The database is accessible online, offering a valuable resource for pathogenomics.

    Conclusions:

    • PAIDB provides a comprehensive resource for studying pathogenicity islands.
    • The integrated database and search tools enhance the identification of PAIs.
    • This resource is vital for advancing pathogenomics and understanding microbial evolution in disease.