Design PCR Primers - Frequently Asked Questions
- Where is Design Primers described?
ES Wright et al. (2014) "Exploiting Extension Bias in PCR to Improve Primer Specificity in Ensembles of Nearly Identical DNA Templates." Environmental Microbiology, doi:10.1111/1462-2920.12259.
- What does the Design Primers web tool do?
Design Primers chooses the most specific sets of forward and reverse primers for targeting amplification of a group of sequences in the presence of multiple non-target groups.
- Can it be used to design primers without any non-target groups?
Yes, Design Primers will choose primers matching the specified constraints with the fewest permutations to achieve maximal coverage of the target group. Simply submit a set of sequences that all share the same target group identifier.
- Can it be used to design primers to differentiate a SNP from the wild-type allele?
Yes, given differently named sequences Design Primers will determine the optimal primer set to use for targeting a specified group. In the case of a SNP the two alleles are already aligned so no additional alignment is required. Simply identify the two sequences differently in the input file and specify the desired design constraints.
- What is the difference between the Design Primers web tool and the DECIPHER program’s DesignPrimers function?
The downloadable program offers control over additional parameters, which makes it more flexible. For example, it allows specification of a region within the sequence alignment to target in primer design. Also, the DECIPHER package for R can handle larger tasks because it imposes no limit on the size of the sequence set or the number of non-target groups.