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A local algorithm for DNA sequence alignment with inversions.

M Schöniger1, M S Waterman

  • 1Department of Mathematics, University of Southern California, Los Angeles 90089-1113.

Bulletin of Mathematical Biology
|July 1, 1992
PubMed
Summary
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This study introduces a novel dynamic programming algorithm for DNA subsequence alignment, incorporating nucleotide substitutions, insertions, deletions, and inversions. The algorithm efficiently identifies optimal alignments with non-intersecting inversions, finding a gene inversion in mitochondrial DNA.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Traditional DNA sequence alignment algorithms primarily consider substitutions, insertions, and deletions.
  • Incorporating inversions (reversed complements) offers a more comprehensive approach to understanding sequence evolution and structure.
  • The computational complexity of alignment with inversions has been a significant challenge.

Purpose of the Study:

  • To develop a dynamic programming algorithm for optimal DNA subsequence alignment that includes inversions.
  • To address the computational efficiency of alignment algorithms by restricting candidate inversions.
  • To identify and analyze non-intersecting inversions within biological sequences.

Main Methods:

  • A dynamic programming approach is employed to find optimal alignments.

Related Experiment Videos

  • Candidate inversions are restricted to the K highest scoring inversions for computational efficiency.
  • An algorithm is presented to find the J best non-intersecting alignments with inversions.

    • Main Results:

    • The algorithm successfully identifies optimal alignments incorporating substitutions, insertions, deletions, and inversions.
    • Application to mitochondrial DNA of Drosophila yakuba and mouse revealed an inversion in the URF6 gene.
    • The study demonstrates the practical utility of the algorithm in biological sequence analysis.

    Conclusions:

    • The developed algorithm provides an efficient method for DNA alignment with inversions.
    • The findings highlight the importance of considering inversions in sequence analysis.
    • Further research into intersecting inversions is warranted.