ArticleNucleic acids research2010
PCRTiler: automated design of tiled and specific PCR primer pairs.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens.Nature communications · 2024Article
- Article
- Smad2/3 Activation Regulates Smad1/5/8 Signaling via a Negative Feedback Loop to Inhibit 3T3-L1 Adipogenesis.International journal of molecular sciences · 2021Article
- Genetic Screening to Identify Candidate Resistance Alleles to Cry1F Corn in Fall Armyworm Using Targeted Sequencing.Insects · 2021Article
- Autism risk in offspring can be assessed through quantification of male sperm mosaicism.Nature medicine · 2020Article
- BRDT is an essential epigenetic regulator for proper chromatin organization, silencing of sex chromosomes and crossover formation in male meiosis.PLoS genetics · 2018Article
- qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms.Nucleic acids research · 2018Article
- ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing.Scientific reports · 2017Article
- Histone H1 and Chromosomal Protein HMGN2 Regulate Prolactin-induced STAT5 Transcription Factor Recruitment and Function in Breast Cancer Cells.The Journal of biological chemistry · 2017Article
- A novel dysferlin mutant pseudoexon bypassed with antisense oligonucleotides.Annals of clinical and translational neurology · 2014Article
- Nucleosomes are stably evicted from enhancers but not promoters upon induction of certain pro-inflammatory genes in mouse macrophages.PloS one · 2014Article
- Genomic analysis of a novel spontaneous albino C57BL/6N mouse strain.Genesis (New York, N.Y. : 2000) · 2013Article
- A robust PCR primer design platform applied to the detection of Acidobacteria Group 1 in soil.Nucleic acids research · 2012Article
- Gemi: PCR primers prediction from multiple alignments.Comparative and functional genomics · 2012Article
- In silico analyses of primers used to detect the pathogenicity genes of Vibrio cholerae.Microbes and environments · 2012Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Efficiency and specificity of PCR amplification is dependent on several parameters, such as amplicon length, as well as hybridization specificity and melting temperature of primer oligonucleotides. Primer design is thus of critical importance for the success of PCR experiments, but can be a time-consuming and repetitive task, for example when large genomic regions are to be scanned for the presence of a protein of interest by chromatin immunoprecipitation experiments. We present here a webserver that allows the automated design of tiled primer pairs for any number of genomic loci. PCRTiler splits the target DNA sequences into smaller regions, and identifies candidate primers for each sub-region by running the well-known program Primer3 followed by the elimination of primers with a high cross-hybridization potential via BLAST. Tiling density and primer characteristics are specified by the user via a simple and user-friendly interface. The webserver can be accessed at http://pcrtiler.alaingervais.org:8080/PCRTiler. Additionally, users may download a standalone Java-based implementation of this software. Experimental validation of PCRTiler has demonstrated that it produces correct results. We have tiled a region of the human genome, in which 96 of 123 primer pairs worked in the first attempt, and 105 of 123 (85%) could be made to work by optimizing the conditions of the PCR assay.
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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.