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

Omar J. Jabado; Gustavo F. Palacios; Vishal Kapoor; Jeffrey Hui; Neil Renwick; Junhui Zhai; Thomas Briese; W. Ian Lipkin

Title:
Greene SCPrimer : a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments
Author(s):
Jabado, Omar J.
Palacios, Gustavo F.
Kapoor, Vishal
Hui, Jeffrey
Renwick, Neil
Zhai, Junhui
Briese, Thomas
Lipkin, W. Ian
Date:
Type:
Articles
Department:
Center for Infection and Immunity
Volume:
34
Permanent URL:
Book/Journal Title:
Nucleic acids research
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.
Subject(s):
Epidemiology
Virology
Publisher DOI:
http://dx.doi.org/10.1093/nar/gkl966
Item views:
670
Metadata:
text | xml

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