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Nucleic Acids Research Advance Access originally published online on November 28, 2006
Nucleic Acids Research 2006 34(22):6605-6611; doi:10.1093/nar/gkl966
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Nucleic Acids Research, 2006, Vol. 34, No. 22 6605-6611
© 2006 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments

Omar J. Jabado, Gustavo Palacios, Vishal Kapoor, Jeffrey Hui, Neil Renwick, Junhui Zhai, Thomas Briese and W. Ian Lipkin*

Jerome L. and Dawn Greene Laboratory for Infectious Diseases, Mailman School of Public Health, Columbia University New York, NY 10032, USA

*To whom correspondence should be addressed. Tel: +1 212 342 9033; Fax: +1 212 342 9044; Email: wil2001{at}columbia.edu

Received May 30, 2006. Revised October 16, 2006. Accepted October 17, 2006.

Polymerase chain reaction (PCR) is widely applied in clinical and environmental microbiology. Primer design is key to the development of successful assays and is often performed manually by using multiple nucleic acid alignments. Few public software tools exist that allow comprehensive design of degenerate primers for large groups of related targets based on complex multiple sequence alignments. Here we present a method for designing such primers based on tree building followed by application of a set covering algorithm, and demonstrate its utility in compiling Multiplex PCR primer panels for detection and differentiation of viral pathogens.

Present address: Jabado Omar, 722 W 168th Street, Room 1801, New York, NY 10032, USA


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