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Computer simulations of theoretical PCR results (Electronic PCR) may be performed to assist in primer design. [14] Touchdown polymerase chain reaction or touchdown style polymerase chain reaction is a method of polymerase chain reaction by which primers will avoid amplifying nonspecific sequences.
OLIGO Primer Analysis Software is a software for DNA primer design. [ 1 ] [ 2 ] The first paper describing this software was published in 1989. [ 3 ] The program is a real time PCR primer and probe search and analysis tool.
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]
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. [7] [8] [9]
The overall success of OE-PCR based DNA assemblies relies on several factors, being the most relevant ones the instrinsic features of the DNA sequence to assemble, the sequence and length of the overlapping overhangs, the design of outer primers for the final amplification and the conditions of the PCR reaction.
Primer Premier is a bioinformatics software used for various PCR applications. It supports the design of degenerate primers for amplifying a related set of nucleotide sequences for the detection of common traits amongst organisms, as well as to determine heredity. [1] The software also designs tagged and nested primers for multiplex PCR ...
Primer walking is an example of directed sequencing because the primer is designed from a known region of DNA to guide the sequencing in a specific direction. In contrast to directed sequencing, shotgun sequencing of DNA is a more rapid sequencing strategy.
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.