Design PCR Primers - Frequently Asked Questions
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.
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.
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.
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.
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.