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Related Experiment Videos

Sorting by restricted-length-weighted reversals.

Thach Cam Nguyen1, Hieu Trung Ngo, Nguyen Bao Nguyen

  • 1Department of Mathematics, National University of Singapore. matnct@nus.edu.sg

Genomics, Proteomics & Bioinformatics
|January 6, 2006
PubMed
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This study introduces a new model for sorting by reversals, prohibiting long reversals to enhance biological relevance. Algorithms are developed to approximate optimal sorting costs for sequences and permutations, offering tight bounds and good approximation ratios.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Algorithm Analysis

Background:

  • The unit-cost model for sorting by reversals lacks biological relevance.
  • Previous extensions used a cost function f(l) = l(alpha) for reversal length l.
  • A need exists for more biologically meaningful and algorithmically general models.

Purpose of the Study:

  • To extend sorting by reversals by prohibiting long reversals.
  • To establish tight or nearly tight bounds for the worst-case cost under the new model.
  • To develop algorithms for approximating optimal sorting costs for 0/1 sequences and permutations.

Main Methods:

  • Introduction of a novel sorting by reversals model where long reversals are prohibited.
  • Application of a cost function f(l) = l(alpha) for permitted reversals.

Related Experiment Videos

  • Development of approximation algorithms for sorting 0/1 sequences and permutations.

    • Main Results:

    • Tight or nearly tight bounds for the worst-case cost of sorting by reversals with prohibited long reversals.
    • Algorithms that approximate the optimal cost for sorting 0/1 sequences and permutations.
    • Demonstration of improved biological meaningfulness and algorithmic generality.

    Conclusions:

    • The proposed model is more biologically meaningful and algorithmically challenging than prior work.
    • The derived bounds are tight or nearly tight, providing accurate worst-case cost estimations.
    • The developed algorithms offer good approximation ratios for practical sorting problems.