Introduction

A polymerase chain reaction (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, for example, when studying a family of genes that is known only in part or is known in a related species. We discuss the complexity of several versions of the problem and give approximation algorithms for one simplified variant. On the basis of these algorithms, we developed a program called HYDEN for designing highly degenerate primers for a set of genomic sequences. We describe HYDEN, and report on its success in several applications for identifying olfactory receptor genes in mammals.

Publications

  1. Degenerate primer design: theoretical analysis and the HYDEN program.
    Cite this
    Linhart C, Shamir R, 2007-01-01 - Methods in molecular biology (Clifton, N.J.)
  2. The degenerate primer design problem: theory and applications.
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    Linhart C, Shamir R, 2005-05-01 - Journal of computational biology : a journal of computational molecular cell biology
  3. The degenerate primer design problem.
    Cite this
    Linhart C, Shamir R, 2002-01-01 - Bioinformatics (Oxford, England)

Credits

  1. Chaim Linhart
    Developer

  2. Ron Shamir
    Investigator

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Summary
AccessionBT000091
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByRon Shamir