ArticleNucleic acids research2009
A thermodynamic approach to PCR primer design.
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 19 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed.
- Targeting surface cell antigen 2 increases sensitivity of Rickettsia typhi detection.PLoS neglected tropical diseases · 2026Article
- Rapid, Economical Detection ofACS omega · 2025Article
- CoMIT: a bioinformatic pipeline for risk-based prediction of COVID-19 test inclusivity.BMC bioinformatics · 2025Article
- Advances in nucleic acid probe-based detection of gene point mutations: a review.Frontiers in chemistry · 2025Review
- ThermoPlex: an automated design tool for target-specific multiplex PCR primers based on DNA thermodynamics.Biology methods & protocols · 2025Article
- Efficient DNA Coding Algorithm for Polymerase Chain Reaction Amplification Information Retrieval.International journal of molecular sciences · 2024Article
- Compartmentalized CRISPR Reactions (CCR) for High-Throughput Screening of Guide RNA Potency and Specificity.bioRxiv : the preprint server for biology · 2024Article
- PCR in Forensic Science: A Critical Review.Genes · 2024Review
- Normalizing real-time PCR results in routine testing.Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2024Article
- The Four mRNA Bases Have Quite Different (Un)folding Free Energies, Applications to RNA Splicing and Translation Initiation with BindOligoNet.Journal of molecular biology · 2022Article
- ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing.Scientific reports · 2017Article
- Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays.PloS one · 2016Article
- A tool for design of primers for microRNA-specific quantitative RT-qPCR.BMC bioinformatics · 2014Article
- Comparative assessment of 5' A/T-rich overhang sequences with optimal and sub-optimal primers to increase PCR yields and sensitivity.Molecular biotechnology · 2013Article
- Patho-Genes.org: a website dedicated to gene sequences of potential bioterror bacteria and PCR primers used to amplify them.Microbial biotechnology · 2012Article
- In silico analyses of primers used to detect the pathogenicity genes of Vibrio cholerae.Microbes and environments · 2012Article
- Troubleshooting fine-tuning procedures for qPCR system design.Journal of clinical laboratory analysis · 2011Article
- pcrEfficiency: a Web tool for PCR amplification efficiency prediction.BMC bioinformatics · 2011Article
- Optimization of turn-back primers in isothermal amplification.Nucleic acids research · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
We developed a primer design method, Pythia, in which state of the art DNA binding affinity computations are directly integrated into the primer design process. We use chemical reaction equilibrium analysis to integrate multiple binding energy calculations into a conservative measure of polymerase chain reaction (PCR) efficiency, and a precomputed index on genomic sequences to evaluate primer specificity. We show that Pythia can design primers with success rates comparable with those of current methods, but yields much higher coverage in difficult genomic regions. For example, in RepeatMasked sequences in the human genome, Pythia achieved a median coverage of 89% as compared with a median coverage of 51% for Primer3. For parameter settings yielding sensitivities of 81%, our method has a recall of 97%, compared with the Primer3 recall of 48%. Because our primer design approach is based on the chemistry of DNA interactions, it has fewer and more physically meaningful parameters than current methods, and is therefore easier to adjust to specific experimental requirements. Our software is freely available at http://pythia.sourceforge.net.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.