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Related Experiment Videos

Concordance analysis of microbial genomes

R E Bruccoleri1, T J Dougherty, D B Davison

  • 1Bristol-Myers Squibb, Pharmaceutical Research Institute, PO Box 4000, Princeton, NJ 08543-4000, USA. bruc@acm.org

Nucleic Acids Research
|September 22, 1998
PubMed
Summary

This study presents a computational tool for identifying conserved microbial proteins, crucial for developing new antimicrobial agents. The system aids in discovering potential drug targets by comparing protein sets across genomes.

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Area of Science:

  • Computational Biology
  • Microbial Genomics
  • Drug Discovery

Background:

  • Conserved proteins across microbial families represent key targets for novel antimicrobial therapies.
  • Identifying these conserved proteins requires efficient comparative genomic tools.

Purpose of the Study:

  • To develop and present a user-friendly computational tool for identifying conserved proteins across specified microbial genomes.
  • To enable the discovery of potential antimicrobial drug targets by highlighting proteins conserved in one set of genomes but absent in another.

Main Methods:

  • Development of a computational tool utilizing a relational database to store protein-coding regions and FASTA comparison results.
  • Implementation of selectable thresholds and homology scoring criteria for user-defined stringency.

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  • Integration of Web technology for sequence retrieval, protein comparison, and multiple sequence alignment (CLUSTALW).

    • Main Results:

    • The database currently contains 97,365 sequences from 19 genomes and 8,798,905 FASTA comparison results.
    • A demonstrated example shows the tool's capability to identify the target of quinolone antibiotics, validating its utility.

    Conclusions:

    • The developed computational tool is effective for identifying conserved microbial proteins with potential as antimicrobial drug targets.
    • The system's flexibility and web-based interface facilitate efficient comparative genomics for drug discovery pipelines.