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DesignSignatures
Automates the process of designing primers for high-resolution melting (HRM), fragment length polymorphism (FLP), and sequencing experiments. DesignSignatures 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 designs primers in three or four steps: (1) designing forward and reverse primers that will efficiently amplify as many input sequences (i.e., alleles) as possible; (2) determining the set of PCR products for each combination of forward and reverse primer; (3) scoring each candidate primer pair based on the diversity of its resulting amplicon signatures in sequencing, FLP, or HRM; (4) optionally, choosing the best restriction enzyme to further maximize signature diversity in FLP or HRM experiments.
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