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Related Experiment Videos

Poxvirus Orthologous Clusters (POCs).

Angelika Ehlers1, John Osborne, Stephanie Slack

  • 1Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.

Bioinformatics (Oxford, England)
|November 9, 2002
PubMed
Summary

Poxvirus Orthologous Clusters (POCs) is a JAVA application that aids in poxvirus genome analysis. It automatically groups orthologous genes, facilitating curator assessment and data retrieval for further study.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Virology

Background:

  • Poxvirus genomes are complex and require specialized tools for analysis.
  • Identifying orthologous genes across poxvirus species is crucial for understanding viral evolution and function.

Purpose of the Study:

  • To introduce Poxvirus Orthologous Clusters (POCs), a JAVA client-server application for poxvirus genome analysis.
  • To provide a user-friendly platform for grouping orthologous genes and retrieving sequence data.

Main Methods:

  • Developed a JAVA client-server application (POCs).
  • Integrated BLASTP for automatic orthologous gene grouping.
  • Implemented complex SQL queries for data retrieval.
  • Included integrated tools for sequence analysis (BLASTP, BLASTX, TBLASTN, Jalview, Dotlet, Laj, NAP).

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Main Results:

  • POCs automatically groups orthologous genes based on BLASTP scores.
  • The application allows retrieval of DNA/protein sequences and gene families via SQL queries.
  • Provides a suite of integrated tools for further sequence interrogation and analysis.

Conclusions:

  • POCs offers a valuable resource for poxvirus genome analysis and curation.
  • The application streamlines the process of identifying and analyzing orthologous genes in poxviruses.