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Oligo Design Overview

DECIPHER includes state-of-the-art methods to accurately predict the hybridization of oligonucleotides to single-stranded DNA or RNA sequences. These methods assist in the design of optimal experiments with a wide variety of objectives, as outlined below:



Design Signatures - Given a FASTA file of unaligned DNA sequences in groups, design PCR primers that will amplify all groups for optimal differentiation with high resolution melting (HRM), fragment length polymorphism (FLP), or sequencing.

DesignSignatures



Design Primers - Given a FASTA file of aligned DNA sequences in groups, design PCR primers that will only amplify one group.

DesignPrimers



Design Probes - Given a FASTA file of aligned RNA sequences in groups, design probes for detection of one group with fluorescent in situ hybridization (FISH).

DesignProbes



ProbeMelt - Given a set of probe and target sequences, predict their melt curves.

ProbeMelt



16S Oligos - Access the database of pre-computed primers and probes targeting the 16S ribosomal RNA.