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A simple algorithm for detecting circular permutations in proteins.

S Uliel1, A Fliess, A Amir

  • 1Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.

Bioinformatics (Oxford, England)
|April 1, 2000
PubMed
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We present a simple and efficient N2 algorithm to detect circular permutation events in proteins, a potential evolutionary mechanism. This method aids in analyzing protein evolution by finding minimal edit distances between circularly permuted sequences.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Circular permutation, where a protein's C-terminus is moved to its N-terminus, can preserve structure and function.
  • This suggests natural circular permutation may have occurred during protein evolution.
  • Detecting such events requires efficient algorithms for large-scale sequence analysis.

Purpose of the Study:

  • To develop an efficient algorithm for detecting circular permutation events in protein sequences.
  • To identify pairs of proteins where one is a circular permutation of the other.
  • To facilitate the study of natural circular permutation as an evolutionary mechanism.

Main Methods:

  • A novel algorithm with N2 time complexity is presented.

Related Experiment Videos

  • The method involves duplicating one sequence and applying a modified dynamic programming approach.
  • This approach aims to find the minimal edit distance between circularly permuted protein sequences.

    • Main Results:

    • An efficient N2 algorithm for detecting circular permutations is described.
    • The algorithm's practical performance is shown to be very good, despite not guaranteeing optimality.
    • A Fortran program is available for calculating optimal edit distances under circular permutation.

    Conclusions:

    • The developed algorithm offers a practical solution for identifying potential natural circular permutation events.
    • This facilitates large-scale evolutionary studies of proteins.
    • Further research can utilize this method to explore the role of circular permutation in protein evolution.