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Super oriented cycles in permutations.

Jayakumar P1, Bhadrachalam Chitturi2

  • 1Department of Computer Science and Applications, Amrita Vishwa Vidyapeetham, Amritapuri, India.

Computers in Biology and Medicine
|September 15, 2023
PubMed
Summary
This summary is machine-generated.

Understanding evolutionary distance requires analyzing genome sequence dissimilarity. This study characterizes super oriented cycles (SOCs) to improve the accuracy of calculating transposition distance between species.

Keywords:
Approximation algorithmsMutationsPermutationsSortingSuper oriented cyclesTranspositionsUpper bound

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Area of Science:

  • Genomics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Evolutionary distance quantifies species dissimilarity using genome sequences.
  • Phylogenetic trees rely on evolutionary distance to depict species relationships.
  • Genome mutations are modeled as permutation transformations.

Purpose of the Study:

  • To characterize super oriented cycles (SOCs) in permutation graphs.
  • To enhance the lower bound calculation for transposition distance.
  • To introduce novel transformations for simplifying permutation analysis.

Main Methods:

  • Modeling genomes as permutations and analyzing their cycle graphs.
  • Defining and identifying odd cycles and super oriented cycles (SOCs).
  • Utilizing equivalent transformations (reduction, (g,b)-split, merge) on permutations.

Main Results:

  • Characterization of super oriented cycles (SOCs) is achieved.
  • Introduction of a novel equivalent transformation called 'merge'.
  • Demonstration that reduction and (g,b)-split preserve transposition distance.

Conclusions:

  • Characterizing SOCs provides a more accurate lower bound for transposition distance.
  • Equivalent transformations simplify complex permutation problems.
  • These findings aid in computing evolutionary distances between species.