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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 84-85

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From page 84...
... Sublinear Similarity Searches The total number N of characters of sequence in biosequence databases is growing exponentially. On the other hand, the size of the query sequences is basically fixed; for example, a protein sequence's length is bounded by 1,500 and averages 300.
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From page 85...
... What we desire is nothing less than algorithms that accomplish exactly the same computational task of complete comparison as the dynamic programming algorithms, but are much faster because the computation is performed in a clever way. A recent result on the approximate suing matching problem under the simple un~t-cost scheme of Figure 3.1 portends the possibility of truly sublinear algorithms for the general problem.
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Key Terms

  • amino acid
  • amino acids
  • query sequence
  • dynamic programming
  • sequence data

  • programming algorithm
  • systolic array
  • protein sequence


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