Summary
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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Notes
- 1.
(See ref. 9 for the definition of the Oh notation)
References
Kwok, S., Chang, S., Sninsky, J., and Wang, A. (1994) A guide to the design and use of mismatched and degenerate primers. PCR Methods and Applications. 3, S39–47.
Linhart, C. and Shamir, R. (2005) The degenerate primer design problem: theory and applications. Journal of Computational Biology 12, 431–456.
Fuchs, T., Malecova, B., Linhart, C., Sharan, R., Khen, M., Herwig, R., Shmulevich, D., Elkon, R., Steinfath, M., O’Brien, J., Radelof, U., Lehrach, H., Lancet, D., and Shamir, R. (2002) DEFOG: a practical scheme for deciphering families of genes. Genomics, 80, 295–302.
Pearson, W., Robins, G., Wredgs, D., and Zhang, T. (1996) On the primer selection problem in polymerase chain reaction experiments. Discrete Applied Mathematics 71, 231–246.
Doi, K. and Imai, H. (1997) Greedy algorithms for finding a small set of primers satisfying cover length resolution conditions in PCR experiments. In Proceedings of 8th Workshop on Genome Informatics, pp. 43–52. Tokyo, Japan.
Bailey, T. and Elkan, C. (1995) Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning 21, 51–80.
Lawrence, C., Altschul, S., Boguski, M., Liu, J., Neuwald, A., and Wootton, J. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262, 208–214.
Linhart, C. (2002) The degenerate primer design problem Masters thesis, School of Computer Science, Tel Aviv University, November 2002. Available at http://www.cs.tau.ac.il/~chaiml/biology/dpd_thesis.ps.gz.
Cormen, T. H., Leiserson, C. E., and Rivest, R. L. (1990) Introduction to Algorithms. MIT Press, Cambridge, Mass.
Souvenir, R., Buhler, J., Stormo, G., and Zhang, W. (2003) Selecting degenerate multiplex PCR primers. In Proceedings of 3rd Workshop on Algorithms in Bioinformatics (WABI 2003), pp. 512–526.
Blum, M., Floyd, R., Pratt, V., Rivest, R., and Tarjan, R. (1973) Time bounds for selection. Journal of Computer and System Sciences 7, 448–461.
Keich, U. and Pevzner, P. (2002) Finding motifs in the twilight zone. In Proceedings of 6th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2002), pp. 195–204.
Linhart, C. and Shamir, R. (2003). HYDEN – A software for designing degenerate primers. Available at http://www.cs.tau.ac.il/~rshamir/hyden.
Radelof, U., Hennig, S., Seranski, P., Steinfath, M., Ramser, J., Reinhardt, R., Poustka, A., Francis, F., and Lehrach, H. (1998) Preselection of shotgun clones by oligonucleotide fingerprinting: an efficient and high throughput strategy to reduce redundancy in large-scale sequencing projects. Nucleic Acids Research 26, 5358–5364.
Sharan, R., Maron-Katz, A., and Shamir, R. (2003) CLICK and EXPANDER: a system for clustering and visualizing gene expression data. Bioinformatics 19, 1787–1799.
Glusman, G., Yanai, I., Rubin, I., and Lancet, D. (2001) The complete human olfactory subgenome. Genome Research 11, 685–702.
Zozulya, S., Echeverri, F., and Nguyen, T. (2001) The human olfactory receptor repertoire. Genome Biology 2, RESEARCH0018.
Buck, L. and Axel, R. (1991) A novel multigene family may encode odorant receptors: a molecular basis for odor recognition. Cell 65, 175–187.
Pilpel, Y. and Lancet, D. (1999) The variable and conserved interfaces of modeled olfactory receptor proteins. Protein Science 8, 969–977.
Fuchs, T., Glusman, G., Horn-Saban, S., Lancet, D., and Pilpel, Y. (2000) The human olfactory subgenome: From sequence to structure and evolution. Human Genetics 108, 1–13.
Olender, T., Fuchs, T., Linhart, C., Shamir, R., Adams, M., Kalush, F., Khen, M., and Lancet, D. (2004) The canine olfactory subgenome. Genomics 83, 361–372.
Young, J., Friedman, C., Williams, E., Ross, J., Tonnes-Priddy, L., and Trask, B. (2002) Different evolutionary processes shaped the mouse and human olfactory receptor gene families. Human Molecular Genetics 11, 535–546.
Zhang, X. and Firestein, S. (2002) The olfactory receptor gene superfamily of the mouse. Nature Neuroscience 5, 124–133.
Gilad, Y., Wiebe, V., Przeworski, M., Lancet, D., and Pääbo, S. (2004) Loss of olfactory receptor genes coincides with the acquisition of full trichromatic vision in primates. PLoS Biology 2, E5.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press
About this protocol
Cite this protocol
Linhart, C., Shamir, R. (2007). Degenerate Primer Design. In: Yuryev, A. (eds) PCR Primer Design. Methods in Molecular Biology™, vol 402. Humana Press. https://doi.org/10.1007/978-1-59745-528-2_11
Download citation
DOI: https://doi.org/10.1007/978-1-59745-528-2_11
Publisher Name: Humana Press
Print ISBN: 978-1-58829-725-9
Online ISBN: 978-1-59745-528-2
eBook Packages: Springer Protocols