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An efficient algorithm for sorting by block-interchanges and its application to the evolution of vibrio species.

Ying Chih Lin1, Chin Lung Lu, Hwan-You Chang

  • 1Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, R.O.C.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|February 24, 2005
PubMed
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This study introduces an efficient algorithm for genome rearrangement using block-interchanges, crucial for understanding chromosome evolution. The method accurately predicts evolutionary relationships in Vibrio pathogens.

Area of Science:

  • Genomics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Genome rearrangement studies explore events like block-interchanges, which swap non-intersecting chromosomal segments.
  • The block-interchange distance problem seeks the minimum number of these events to transform one chromosome into another.

Purpose of the Study:

  • To develop an efficient algorithm for solving the block-interchange distance problem on circular chromosomes.
  • To extend the algorithm to linear chromosomes and apply it to analyze evolutionary relationships.

Main Methods:

  • Utilized permutation groups from algebra to devise a novel algorithm.
  • The algorithm achieves a time complexity of O(delta*n), where n is chromosome length and delta is the minimum block-interchanges.
  • Pre-calculation of delta in O(n) time is incorporated.

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Main Results:

  • Developed and implemented an O(delta*n) algorithm for circular chromosome rearrangement.
  • Extended the methodology to linear chromosomes, yielding analogous results.
  • Applied the algorithm to circular genomes of three Vibrio pathogens.

Conclusions:

  • The block-interchange algorithm accurately predicted evolutionary relationships among Vibrio species.
  • Experimental results align with previous findings, suggesting block-interchanges are significant in Vibrio evolution.