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Related Experiment Videos

PhyloGenie: automated phylome generation and analysis.

Tancred Frickey1, Andrei N Lupas

  • 1Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, Spemannstr. 35, D-72076 Tuebingen, Germany.

Nucleic Acids Research
|October 2, 2004
PubMed
Summary

Automated phylome analysis enables large-scale evolutionary studies. This approach accurately identifies homologous relationships and reveals insights into genome evolution, such as gene duplication events.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Phylogenetic reconstruction is crucial for determining sequence homology but is often limited to single genes due to alignment and automation challenges.
  • Analyzing entire proteomes (phylomes) requires extensive automation for sequence selection, alignment, inference, and tree analysis.

Purpose of the Study:

  • To present a suite of programs for automating phylome generation and analysis.
  • To develop a tool for extracting specific phylogenies from a tree database based on topological constraints.

Main Methods:

  • Development of automated software for phylome construction from seed sequences to phylogenetic trees.
  • Implementation of a utility for querying tree databases using topological constraints.

Related Experiment Videos

  • Application of phylome analysis to Thermoplasma acidophilum and Danio rerio proteomes.

    • Main Results:

    • Phylome analysis of Thermoplasma acidophilum revealed protein phylogenies to be more reliable than BLAST hits for detecting lateral gene transfer.
    • Phylome analysis of Danio rerio identified over twice the previously known proteins, supporting an additional genome duplication in actinopterygians.

    Conclusions:

    • Automated phylome analysis is essential for large-scale evolutionary studies.
    • Phylome-based methods offer superior accuracy for evolutionary event detection compared to sequence similarity searches.
    • Phylome analysis provides novel insights into genome evolution and duplication events.