Multiplexing Short Primers for Viral Family PCR

We describe a Multiplex Primer Prediction (MPP) algorithm to build multiplex compatible primer sets for large, diverse, and unalignable sets of target sequences. The MPP algorithm is scalable to larger target sets than other available software, and it does not require a multiple sequence alignment....

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Bibliographic Details
Published in:Nucleic acids research 2008-06
Main Authors: Gardner, S N, Hiddessen, A L, Hara, C A, Williams, P L, Wagner, M, Colston, B W
Format: Article
Language:English
Subjects:
ALGORITHMS
ALIGNMENT
BASIC BIOLOGICAL SCIENCES
DETECTION
DISEASES
FORECASTING
GENERAL AND MISCELLANEOUS
HEMAGGLUTININS
INFLUENZA
TARGETS
VIRUSES
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Summary:We describe a Multiplex Primer Prediction (MPP) algorithm to build multiplex compatible primer sets for large, diverse, and unalignable sets of target sequences. The MPP algorithm is scalable to larger target sets than other available software, and it does not require a multiple sequence alignment. We applied it to questions in viral detection, and demonstrated that there are no universally conserved priming sequences among viruses and that it could require an unfeasibly large number of primers ({approx}3700 18-mers or {approx}2000 10-mers) to generate amplicons from all sequenced viruses. We then designed primer sets separately for each viral family, and for several diverse species such as foot-and-mouth disease virus, hemagglutinin and neuraminidase segments of influenza A virus, Norwalk virus, and HIV-1.
ISSN:0305-1048
1362-4962