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Related Experiment Videos

Walking through protein sequence space.

Zakharia M Frenkel1, Edward N Trifonov

  • 1Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel. zakharf@research.haifa.ac.il <zakharf@research.haifa.ac.il>

Journal of Theoretical Biology
|September 6, 2006
PubMed
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A new tool enables "space walks" through protein sequence space, identifying evolutionary relatives. This method reveals significant sequence divergence and aids in protein evolution studies and annotation.

Area of Science:

  • Evolutionary biology
  • Bioinformatics
  • Computational biology

Background:

  • The concept of protein sequence space, originally proposed by Maynard Smith, is crucial for understanding protein evolution.
  • Exploring evolutionary relationships between protein sequences is fundamental for biological research.

Purpose of the Study:

  • To develop a novel computational tool for navigating the protein sequence space.
  • To enable the identification of likely evolutionary relatives of protein sequences.
  • To explore the extent of sequence divergence possible through evolutionary walks.

Main Methods:

  • Development of a novel computational tool for "space walking" between protein sequences.
  • Utilizing a defined threshold of sequence identity for consecutive steps in the walk.

Related Experiment Videos

  • Analysis of sequence space using randomized (shuffled) sequences as a control.

    • Main Results:

    • The developed tool successfully facilitates "space walks" between protein sequences.
    • Walks of many steps are possible at a given identity threshold, allowing substantial sequence divergence.
    • In contrast, "space walks" in randomized sequence spaces are significantly shorter.

    Conclusions:

    • The novel "space walk" approach opens new perspectives for protein evolutionary studies.
    • This method offers a valuable tool for sequence annotation and understanding evolutionary trajectories.
    • The findings highlight the potential for significant sequence divergence over evolutionary pathways.