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:

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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.

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

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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).

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

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