Enhancements and modifications of primer design program Primer3
By Triinu Koressaar, Maido Remm. Bioinform., 2007
2,591 citations recorded by the source corpus.
UNLABELLED The determination of annealing temperature is a critical step in PCR design. This parameter is typically derived from the melting temperature of the PCR primers, so for successful PCR work it is important to determine the melting temperature of primer accurately. We introduced several enhancements in the widely used primer design program Primer3. The improvements include a formula for calculating melting temperature and a salt correction formula. Also, the new version can take into account the effects of divalent cations, which are included in most PCR buffers. Another modification enables using lowercase masked template sequences for primer design. AVAILABILITY Features described in this article have been implemented into the development code of Primer3 and will be available in future versions (version 1.1 and newer) of Primer3. Also, a modified version is compiled under the name of mPrimer3 which is distributed independently. The web-based version of mPrimer3 is available at http://bioinfo.ebc.ee/mprimer3/ and the binary code is freely downloadable from the URL http://bioinfo.ebc.ee/download/.
Subfields: Biomedical Engineering, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/041e51b7931029b468bb13e28afda9208c8fa78d
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Citations in the corpus
- BatchPrimer3: A high throughput web application for PCR and sequencing primer design (2008, methodology): “An additional T m calculation module was implemented for SNP genotyping primers and sequencing primers based on the same model of the nearest neighbour thermodynamic theory [18,19] as used in the Primer3 core program (v 1.1) [4].”
- Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications (2014, methodology): “42,43; version 2.3.5) using Tm 63, primer length 25–30 bp and product size ranging from 350– 700 bp and avoiding common SNPs.”
- Quantification of bacterial non-specific acid (phoC) and alkaline (phoD) phosphatase genes in bulk and rhizosphere soil from organically managed soybean fields (2017, methodology): “Primers were identified using CEMAsuite which includes a version of primer3 (Koressaar and Remm, 2007; Untergasser et al., 2012), and selected based on binding at active site residues as outlined previously (Martinez et al.”
- Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea (2019, background): “0 (Koressaar and Remm, 2007) to verify the match between primers and the target region.”