DesignSignatures: a tool for designing primers that yields amplicons with distinct signatures.

Abstract

For numerous experimental applications, PCR primers must be designed to efficiently amplify a set of homologous DNA sequences while giving rise to amplicons with maximally diverse signatures. We developed DesignSignatures to automate the process of designing primers for high-resolution melting (HRM), fragment length polymorphism (FLP) and sequencing experiments. The program also finds the best restriction enzyme to further diversify HRM or FLP signatures. This enables efficient comparison across many experimental designs in order to maximize signature diversity. DesignSignatures is accessible as a web tool at www.DECIPHER.cee.wisc.edu, or as part of the DECIPHER open source software package for R available from BioConductor. kalin@discovery.wisc.edu Supplementary data are available at Bioinformatics online.