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Primer3 is a program for designing PCR primers (PCR = "Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.
Primer3 was a complete re-implementation of an earlier program: Primer 0.5 (Steve Lincoln, Mark Daly, and Eric S. Lander). Primer3 web service at primer3.ut.ee is a part of services provided by ELIXIR - European research infrastructure for biological information.
Primer3Plus picks primers from a DNA sequence using Primer3. This is the latest version straight from the developers with all the new features.
Primer3Plus. Select primer pairs to detect the given template sequence. Optionally targets and included/excluded regions can be specified. Mark an included region to pick primers fixed at its the boundaries. The quality of the primers might be low. Pick a series of primers on both strands for sequencing.
Primer3 was a complete re-implementation of an earlier program: Primer 0.5 (Steve Lincoln, Mark Daly, and Eric S. Lander). Lincoln Stein championed the idea of making Primer3 a software component suitable for high-throughput primer design.
Primer3 converts concentration of divalent cations to concentration of monovalent cations using formula suggested in the paper Ahsen et al., 2001. [Monovalent cations] = [Monovalent cations] + 120*(v([divalent cations] - [dNTP])).
Primer3 picks primers for PCR reactions, considering as criteria: o oligonucleotide melting temperature, size, GC content, and primer-dimer possibilities, o PCR product size, o positional constraints within the source (template) sequence, and o possibilities for ectopic priming (amplifying the wrong sequence) o many other constraints.
Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3"). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl.
There are several available versions of the Primer3 web interface: Primer3Web and Primer3Plus.
Jun 21, 2012 · Reliable primer design is crucial for successful PCR, and for over a decade, the open-source Primer3 software has been widely used for primer design, often in high-throughput genomics applications. It has also been incorporated into numerous publicly available software packages and web services.
