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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 76-77

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From page 76...
... So in practice, evolutionary biologists have put a great deal of effort into designing heuristic algorithms for the phylogeny problem, and there is much debate about which of these is best. K-Best Alignments The alignment aIgonthm in the section "The Basic Dynamic Programming Algorithm" above reports an optimal alignment that is clearly a function of the choice of scoring scheme.
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From page 77...
... comparing the a and ,8 chicken hemoglobin chains. For a setting of the gap costs that gave the biologically correct alignment, there were 17 optimal alignments, 1,317 alignments within 5 percent of the optimum, and 20,137,655 within 20 percent of the optimum.
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Key Terms

  • scoring scheme
  • edit graph
  • gap costs
  • dynamic programming
  • multiple sequence

  • optimal alignments
  • optimal alignment
  • programming algorithm
  • pairwise alignments
  • scoring schemes

  • basic dynamic
  • alignment score
  • sequence alignment
  • gap cost


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