ArticleNucleic acids research2009
Multiplex primer prediction software for divergent targets.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Article
- Modeling the Amplification of Immunoglobulins through Machine Learning on Sequence-Specific Features.Scientific reports · 2019Article
- MRPrimer: a MapReduce-based method for the thorough design of valid and ranked primers for PCR.Nucleic acids research · 2015Article
- Gemi: PCR primers prediction from multiple alignments.Comparative and functional genomics · 2012Article
- Skip the alignment: degenerate, multiplex primer and probe design using K-mer matching instead of alignments.PloS one · 2012Article
- Viral nucleic acids in live-attenuated vaccines: detection of minority variants and an adventitious virus.Journal of virology · 2010Article
- MPprimer: a program for reliable multiplex PCR primer design.BMC bioinformatics · 2010Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We describe a Multiplex Primer Prediction (MPP) algorithm to build multiplex compatible primer sets to amplify all members of 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 ( approximately 3700 18-mers or approximately 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 (FMDV), hemagglutinin (HA) and neuraminidase (NA) segments of influenza A virus, Norwalk virus, and HIV-1. We empirically demonstrated the application of the software with a multiplex set of 16 short (10 nt) primers designed to amplify the Poxviridae family to produce a specific amplicon from vaccinia virus.
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Registered trials
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