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, W. Ian Lipkin

Research output: Contribution to journalArticlepeer-review

61 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)6605-6611
Number of pages7
JournalNucleic Acids Research
Volume34
Issue number22
DOIs
StatePublished - Dec 2006
Externally publishedYes

Fingerprint

Dive into the research topics of 'Greene SCPrimer: A rapid comprehensive tool for designing degenerate primers from multiple sequence alignments'. Together they form a unique fingerprint.

Cite this