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Calculating the Secrets of Life Contributions of the Mathematical Sciences to Molecular Biology (1995) / Chapter Skim
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Pages 73-75

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From page 73...
... Thus calling this measure a distance is formally correct for a wide class of scoring schemes d. Immediately note that the distance and similarity perspectives are complementary.
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From page 74...
... The problem of finding a maximum (minimum) -scoring alignment among K sequences can be solved by extending the dynamic programming recurrence for the basic problem from a recurrence over a two-dimensional matrix to a recurrence over a K-rlimensional matnx.
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From page 75...
... Thus many authors have sought heuristic approximations, the most popular of which is to take o(K2N2 ~ time to compute all pairwise optimal alignments between the K sequences, and then produce a multiple sequence alignment by merging these pairwise alignments. Note that any multiple sequence alignment induces an alignment between a given pair of sequences (take the two rows of the tableau and remove any columns consisting of just dashes)
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Key Terms

  • scoring scheme
  • sequence comparison
  • dynamic programming
  • multiple sequence
  • optimal alignments

  • optimal alignment
  • sequence data
  • pairwise alignments
  • scoring schemes
  • sequence alignment


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