The Degenerate Primer Design Problem: Theory and Applications

  title={The Degenerate Primer Design Problem: Theory and Applications},
  author={Chaim Linhart and Ron Shamir},
  journal={Journal of computational biology : a journal of computational molecular cell biology},
  volume={12 4},
A PCR primer sequence is called degenerate if some of its positions have several possible bases. The degeneracy of the primer is the number of unique sequence combinations it contains. We study the problem of designing a pair of primers with prescribed degeneracy that match a maximum number of given input sequences. Such problems occur when studying a family of genes that is known only in part, or is known in a related species. We prove that various simplified versions of the problem are hard… CONTINUE READING
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