ArticleNucleic acids research2016
MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Stepwise Optimization of Real-Time RT-PCR Analysis.Methods in molecular biology (Clifton, N.J.) · 2023Article
- The macrophage odorant receptor Olfr78 mediates the lactate-induced M2 phenotype of tumor-associated macrophages.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- An optimized protocol for stepwise optimization of real-time RT-PCR analysis.Horticulture research · 2021Article
- GPrimer: a fast GPU-based pipeline for primer design for qPCR experiments.BMC bioinformatics · 2021Article
- Article
- MRPrimerW2: an enhanced tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments.Nucleic acids research · 2019Article
- PCRdrive: the largest qPCR assay archive to date and endless potential for lab workflow revitalization.BMC bioinformatics · 2018Article
- Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements.FEMS microbiology ecology · 2018Article
- qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms.Nucleic acids research · 2018Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Design of high-quality primers for multiple target sequences is essential for qPCR experiments, but is challenging due to the need to consider both homology tests on off-target sequences and the same stringent filtering constraints on the primers. Existing web servers for primer design have major drawbacks, including requiring the use of BLAST-like tools for homology tests, lack of support for ranking of primers, TaqMan probes and simultaneous design of primers against multiple targets. Due to the large-scale computational overhead, the few web servers supporting homology tests use heuristic approaches or perform homology tests within a limited scope. Here, we describe the MRPrimerW, which performs complete homology testing, supports batch design of primers for multi-target qPCR experiments, supports design of TaqMan probes and ranks the resulting primers to return the top-1 best primers to the user. To ensure high accuracy, we adopted the core algorithm of a previously reported MapReduce-based method, MRPrimer, but completely redesigned it to allow users to receive query results quickly in a web interface, without requiring a MapReduce cluster or a long computation. MRPrimerW provides primer design services and a complete set of 341 963 135 in silico validated primers covering 99% of human and mouse genes. Free access: http://MRPrimerW.com.
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