Design Signatures - Frequently Asked Questions
Wright, E. S., & Vetsigian, K. H. (2016) "DesignSignatures: a tool for designing primers that yields amplicons with distinct signatures." Bioinformatics, doi:10.1093/bioinformatics/btw047.
Design Signatures assists in finding the optimal pair of forward and reverse primers to obtain a distinct "signature" from each input group (i.e., sequence). After PCR, the amplicons' signatures can be distinguished using either High Resolution Melting (HRM) analysis, Fragment Length Polymorphism (FLP) analysis, or sequencing. The tool can also find the best restriction enzyme to further diversify the signatures for either RFLP or Restriction HRM.
Design Signatures was created to perform the most common primer design tasks, which share the objective of differentiating groups based on their unique signatures. The primers it generates are designed to target as many groups (i.e., alleles) as possible using conserved sequences, while amplifying variability that will result in different signatures.
The downloadable program offers control over additional parameters, which makes it more flexible. However, for most user's applications the web tool's defaults will be sufficient. The DECIPHER package for R can handle larger tasks because it has no limit on the size of the sequence set or the number of enzymes. Also, DECIPHER has additional functionality for delving further into the outputs of DesignSignatures.