ArticleNucleic acids research2019
MFEprimer-3.0: quality control for PCR primers.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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51 citing papers in PubMed.
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- Phytochrome-mediated light perception in dodders drives haustorium development through epigenetic mechanisms.Plant & cell physiology · 2026Article
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- A de novo start-loss variant in the NIPBL gene causing mild type 1 Cornelia de Lange syndrome in an Iranian family: A Case Report.Journal of medical case reports · 2026Article
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- Accelerating primer design for amplicon sequencing using large language model-powered agents.Nature biomedical engineering · 2026Article
- From Triplex to Quadruplex: Enhancing CDC's Respiratory qPCR Assay with RSV Detection on Panther FusionMicroorganisms · 2026Article
- Multiplex Quantification of 19 GM Soybean Lines Using Digital PCR.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Multiplexed Digital PCR for Evaluation of Karyotype Quality of Mouse Embryonic Stem Cells.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Engineered crRNA Drives RPA-T7-CRISPR/Cas14a Cascade for Ultrasensitive Detection of ctDNA PIK3CA H1047R.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- A non-invasive method to genotype cephalopod sex by quantitative PCR.bioRxiv : the preprint server for biology · 2025Article
- High Concordance Between SYBR Green and TaqMan PCR for SARS-CoV-2 Detection in Nasopharyngeal and Saliva Samples.Viruses · 2025Article
- Synthesis of large single-transcript pathways from oligonucleotide pools: Design of STARBURST, an autobioluminescent reporter.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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- Investigating Single-Molecule Molecular Inversion Probes for Medium-Scale Targeted DNA Methylation Analysis.Epigenomes · 2025Article
- MiPRIME: an integrated and intelligent platform for mining primer and probe sequences of microbial species.Bioinformatics (Oxford, England) · 2024Article
- High resolution mapping of a novel non-transgressive hybrid susceptibility locus in barley exploited by P. teres f. maculata.BMC plant biology · 2024Article
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Quality control (QC) for lab-designed primers is crucial for the success of a polymerase chain reaction (PCR). Here, we present MFEprimer-3.0, a functional primer quality control program for checking non-specific amplicons, dimers, hairpins and other parameters. The new features of the current version include: (i) more sensitive binding site search using the updated k-mer algorithm that allows mismatches within the k-mer, except for the first base at the 3' end. The binding sites of each primer with a stable 3' end are listed in the output; (ii) new algorithms for rapidly identifying self-dimers, cross-dimers and hairpins; (iii) the command-line version, which has an added option of JSON output to enhance the versatility of MFEprimer by acting as a QC step in the 'primer design → quality control → redesign' pipeline; (iv) a function for checking whether the binding sites contain single nucleotide polymorphisms (SNPs), which will affect the consistency of binding efficiency among different samples. In summary, MFEprimer-3.0 is updated with the well-tested PCR primer QC program and it can be integrated into various PCR primer design applications as a QC module. The MFEprimer-3.0 server is freely accessible without any login requirement at: https://mfeprimer3.igenetech.com/ and https://www.mfeprimer.com/. The source code for the command-line version is available upon request.
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