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Nucleic Acids Res. 2006;34(22):6605-11. Epub 2006 Nov 28.

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

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  • 1Jerome L. and Dawn Greene Laboratory for Infectious Diseases, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.


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.

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