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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 82-83

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From page 82...
... In DNA databases, the entries are typically much longer than the query sequence, and one is looking for subsegments of the entry that match the query. Heuristic Algorithms The problem of searching for protein sim~lanties efficiently has led many investigators to abandon dynamic programming algorithms (for which the size of the problem has become too large)
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From page 83...
... The dynamic programming algorithm for local similarities presented above (also known as the Smith-Waterman algorithms takes roughly 1000.0N microseconds to search a database with a total of N characters in it. On the other hand, FASTA takes 20.0N microseconds, and BLASTA only about 2.0N microseconds.
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Key Terms

  • segment pair
  • segment pairs
  • query sequence
  • dynamic programming
  • programming algorithm

  • systolic array
  • local similarities


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