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Bioinformatics Vol. 18 no. 90001 2002
Pages S172-S181
© 2002 Oxford University Press

The degenerate primer design problem

Chaim Linhart and Ron Shamir

School Of Computer Science, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel

Received on January 24, 2002 ; revised on April 1, 2002 ; accepted on April 1, 2002

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, show the polynomiality of some restricted cases, and develop approximation algorithms for one variant. Based on these algorithms, we implemented a program called HYDEN for designing highly-degenerate primers for a set of genomic sequences. We report on the success of the program in an experimental scheme for identifying all human olfactory receptor (OR) genes. In that project, HYDEN was used to design primers with degeneracies up to 1010 that amplified with high specificity many novel genes of that family, tripling the number of OR genes known at the time.

Availability: Available on request from the authors.

Contact: chaiml{at}tau.ac.il; rshamir{at}tau.ac.il

Keywords: PCR primer design; degenerate primers; optimization; human olfactory subgenome; protein families.


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