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The design of appropriate short or long primer pairs is only one goal of PCR product prediction. Other information provided by in silico PCR tools may include determining primer location, orientation, length of each amplicon , simulation of electrophoretic mobility, identification of open reading frames , and links to other web resources.
The free NCBI tool Primer-BLAST integrates primer design and BLAST search into one application, [6] as do commercial software products such as ePrime and Beacon Designer. Computer simulations of theoretical PCR results (Electronic PCR) may be performed to assist in primer design by giving melting and annealing temperatures, etc. [7]
Beacon Designer designs primers and probes for real-time PCR (polymerase chain reaction) assays.It is compatible to work on Windows as well as on Mac. The software currently supports the following real-time PCR chemistries for primer and probe design:
Primer dimer formation often competes with formation of the DNA fragment of interest, and may be avoided using primers that are designed such that they lack complementarity—especially at the 3' ends—to itself or the other primer used in the reaction. If primer design is constrained by other factors and if primer-dimers do occur, methods to ...
eDNA metabarcoding has applications to diversity monitoring across all habitats and taxonomic groups, ancient ecosystem reconstruction, plant-pollinator interactions, diet analysis, invasive species detection, pollution responses, and air quality monitoring. eDNA metabarcoding is a unique method still in development and will likely remain in flux for some time as technology advances and ...
For this reason, it is critical to accurately predict the melting curve of PCR products when designing primers that will distinguish sequence variants. Specialty software, such as uMelt [13] and DesignSignatures, [14] are available to help design primers that will maximize melting curve variability specifically for high-resolution melting assays.
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