Oligo Design Overview

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

Why use DECIPHER for oligo design?

• DECIPHER contains many powerful tools for a wide variety of oligo design tasks.
• Unlike other popular approaches, each of DECIPHER's oligo design functions uses state-of-the-art free energy based prediction of hybridization.
• Both hybridization and elongation efficiency are considered when designing PCR primers.
• DECIPHER's oligo design tools are designed to handle large-scale and challenging design problems.

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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.