ArticleBMC bioinformatics2010
MPprimer: a program for reliable multiplex PCR primer design.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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Who cites it
74 citing papers in PubMed.
- Primer design through submodular function estimation.Bioinformatics (Oxford, England) · 2026Article
- Multiplex PCR for differentiating Ornithodoros tick vectors in South Africa: Proof of concept.The Onderstepoort journal of veterinary research · 2025Article
- Prevalence of resistance markers of artemisinin, partner drugs, and sulfadoxine-pyrimethamine in Nanyumbu and Masasi Districts, Tanzania between 2020 and 2021.Antimicrobial agents and chemotherapy · 2025Article
- Smart-Plexer 2.0: Leveraging New Features of Amplification Curves to Enhance the Selection of Multiplex PCR Assays in Multi-Target Identification.Analytical chemistry · 2025Article
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- The Use of Gel Electrophoresis to Separate Multiplex Polymerase Chain Reaction Amplicons Allows for the Easy Identification and Assessment of the Spread of ToxigenicGels (Basel, Switzerland) · 2024Article
- Development of a novel five dye insertion/deletion (INDEL) panel for ancestry determination.International journal of legal medicine · 2024Article
- Development of Multiplex RT qPCR Assays for Simultaneous Detection and Quantification of Faecal Indicator Bacteria in Bathing Recreational Waters.Microorganisms · 2024Article
- Development of two multiplex PCR assays for rapid detection of eleven Gram-negative bacteria in children with septicemia.Tropical medicine and health · 2024Article
- Circulating Nucleic Acids in Colorectal Cancer: Diagnostic and Prognostic Value.Disease markers · 2024Review
- A reliable and quick method for screening alternative splicing variants for low-abundance genes.PloS one · 2024Article
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- A Multiplex PCR Method for Simultaneous Detection of Infectious Laryngotracheitis Virus andVeterinary sciences · 2023Article
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- Curcumin supplementation increases longevity and antioxidant capacity inFrontiers in pharmacology · 2023Article
- High-throughput primer design by scoring in piecewise logistic model for multiple polymerase chain reaction variants.Scientific reports · 2022Article
- Recent trends and developments of PCR-based methods for the detection of food-borneJournal of food science and technology · 2022Review
- High genetic differentiation of Indo-Pacific humpback dolphins (Ecology and evolution · 2022Article
14 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMultiplex PCR, defined as the simultaneous amplification of multiple regions of a DNA template or multiple DNA templates using more than one primer set (comprising a forward primer and a reverse primer) in one tube, has been widely used in diagnostic applications of clinical and environmental microbiology studies. However, primer design for multiplex PCR is still a challenging problem and several factors need to be considered. These problems include mis-priming due to nonspecific binding to non-target DNA templates, primer dimerization, and the inability to separate and purify DNA amplicons with similar electrophoretic mobility.
resultsA program named MPprimer was developed to help users for reliable multiplex PCR primer design. It employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. The graph-expanding algorithm derived from the greedy algorithm was used to determine the optimal primer set combinations (PSCs) for multiplex PCR assay. In addition, MPprimer provides a virtual electrophotogram to help users choose the best PSC. The experimental validation from 2x to 5x plex PCR demonstrates the reliability of MPprimer. As another example, MPprimer is able to design the multiplex PCR primers for DMD (dystrophin gene which caused Duchenne Muscular Dystrophy), which has 79 exons, for 20x, 20x, 20x, 14x, and 5x plex PCR reactions in five tubes to detect underlying exon deletions.
conclusionsMPprimer is a valuable tool for designing specific, non-dimerizing primer set combinations with constrained amplicons size for multiplex PCR assays.
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