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

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 deg...

Full description

Bibliographic Details
Main Authors:	Jabado, Omar J., Palacios, Gustavo, Kapoor, Vishal, Hui, Jeffrey, Renwick, Neil, Zhai, Junhui, Briese, Thomas, Lipkin, W. Ian
Format:	Online
Language:	English
Published:	Oxford University Press 2006
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1747188/

id	pubmed-1747188
recordtype	oai_dc
spelling	pubmed-17471882006-12-26 Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments Jabado, Omar J. Palacios, Gustavo Kapoor, Vishal Hui, Jeffrey Renwick, Neil Zhai, Junhui Briese, Thomas Lipkin, W. Ian Computational Biology 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. Oxford University Press 2006-12 2006-11-28 /pmc/articles/PMC1747188/ /pubmed/17135211 http://dx.doi.org/10.1093/nar/gkl966 Text en © 2006 The Author(s).
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Jabado, Omar J. Palacios, Gustavo Kapoor, Vishal Hui, Jeffrey Renwick, Neil Zhai, Junhui Briese, Thomas Lipkin, W. Ian
spellingShingle	Jabado, Omar J. Palacios, Gustavo Kapoor, Vishal Hui, Jeffrey Renwick, Neil Zhai, Junhui Briese, Thomas Lipkin, W. Ian Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments
author_facet	Jabado, Omar J. Palacios, Gustavo Kapoor, Vishal Hui, Jeffrey Renwick, Neil Zhai, Junhui Briese, Thomas Lipkin, W. Ian
author_sort	Jabado, Omar J.
title	Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments
title_short	Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments
title_full	Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments
title_fullStr	Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments
title_full_unstemmed	Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments
title_sort	greene scprimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments
description	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.
publisher	Oxford University Press
publishDate	2006
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1747188/
_version_	1611392374953476096

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

Similar Items