ArticleBMC bioinformatics2011
pcrEfficiency: a Web tool for PCR amplification efficiency prediction.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
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- Predicting sequence-specific amplification efficiency in multi-template PCR with deep learning.Nature communications · 2025Article
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- Validation of a bitmap of genes involved in cherry fruit cracking by digital PCR and qPCR, suitable for plant breeding.Scientific reports · 2025Article
- MMTV RNA packaging requires an extended long-range interaction for productive Gag binding to packaging signals.PLoS biology · 2024Article
- Cecropin A Alleviates LPS-Induced Oxidative Stress and Apoptosis of Bovine Endometrial Epithelial Cells.Animals : an open access journal from MDPI · 2024Article
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- A digital twin for DNA data storage based on comprehensive quantification of errors and biases.Nature communications · 2023Article
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- The transcription factors VaERF16 and VaMYB306 interact to enhance resistance of grapevine to Botrytis cinerea infection.Molecular plant pathology · 2022Article
- Aberrant Whole Blood Gene Expression in the Lumen of Human Intracranial Aneurysms.Diagnostics (Basel, Switzerland) · 2021Article
- Genetic barcodes allow traceability of CRISPR/Cas9-derived Aspergillus niger strains without affecting their fitness.Current genetics · 2021Article
- Classification models using circulating neutrophil transcripts can detect unruptured intracranial aneurysm.Journal of translational medicine · 2020Article
- The clock gene Gigantea 1 from Petunia hybrida coordinates vegetative growth and inflorescence architecture.Scientific reports · 2020Article
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- Investigating appropriate molecular and chemical methods for ingredient identity testing of plant-based protein powder dietary supplements.Scientific reports · 2019Article
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- Effects of unpaired 1 gene overexpression on the lifespan of Drosophila melanogaster.BMC systems biology · 2019Article
- A novel data processing method CyC* for quantitative real time polymerase chain reaction minimizes cumulative error.PloS one · 2019Article
- Expression patterns of candidate genes reflecting the growth performance of goats subjected to heat stress.Molecular biology reports · 2018Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundRelative calculation of differential gene expression in quantitative PCR reactions requires comparison between amplification experiments that include reference genes and genes under study. Ignoring the differences between their efficiencies may lead to miscalculation of gene expression even with the same starting amount of template. Although there are several tools performing PCR primer design, there is no tool available that predicts PCR efficiency for a given amplicon and primer pair.
resultsWe have used a statistical approach based on 90 primer pair combinations amplifying templates from bacteria, yeast, plants and humans, ranging in size between 74 and 907 bp to identify the parameters that affect PCR efficiency. We developed a generalized additive model fitting the data and constructed an open source Web interface that allows the obtention of oligonucleotides optimized for PCR with predicted amplification efficiencies starting from a given sequence.
conclusionspcrEfficiency provides an easy-to-use web interface allowing the prediction of PCR efficiencies prior to web lab experiments thus easing quantitative real-time PCR set-up. A web-based service as well the source code are provided freely at http://srvgen.upct.es/efficiency.html under the GPL v2 license.
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