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Phylogenetic web profiler.

Philip Wong1, Grigory Kolesov, Dmitrij Frishman

  • 1Department of Biochemistry, University of Toronto, Medical Sciences Building, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.

Bioinformatics (Oxford, England)
|April 15, 2003
PubMed
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Phylogenetic Web Profiler (PWP) is a new web service for protein phylogenetic profiling. It allows flexible ortholog prediction and analysis of functional linkage between proteins using extensive genome data.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Phylogenetic profiling is crucial for inferring protein function.
  • Existing tools lack flexibility in ortholog prediction parameters.
  • Integration with comprehensive genome databases is limited.

Purpose of the Study:

  • To introduce Phylogenetic Web Profiler (PWP), a novel web-based service.
  • To provide a flexible platform for phylogenetic profiling of proteins.
  • To facilitate the analysis of functional linkage between proteins.

Main Methods:

  • Developed a web-based service, Phylogenetic Web Profiler (PWP).
  • Integrated PWP with the PEDANT genome database, including 63 completed genomes and plasmids.
  • Implemented adjustable ortholog prediction parameters: E-value cutoff, length difference tolerance, and annotation similarity.

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Main Results:

  • PWP offers a user-friendly interface for phylogenetic profiling.
  • The tool supports customizable ortholog prediction, enhancing accuracy.
  • Features include seamless integration with PEDANT and analysis tools for protein properties.

Conclusions:

  • Phylogenetic Web Profiler (PWP) is a valuable tool for bioinformatics research.
  • Its flexibility and integration capabilities aid in understanding protein functional linkage.
  • PWP enhances the analysis of protein families across diverse genomes.