OligoDesign — Oligo Design Evaluator
Paste any oligo — hand-designed or generated by a tool — and get a structured evaluation: a verdict, risk drivers, recommended actions and explicit assumptions. Tm uses the same nearest-neighbor model and salt correction as Primer3; hairpin and dimer free energies come from a nearest-neighbor fold; thresholds are taken from published design guidelines.
Single Oligo Judge — Evaluate one primer or probe sequence: role-aware oligo design evaluation covering Tm, GC content, hairpins, self-dimers, and 3′ clamp quality, with a structured verdict.Primer Pair Judge — Evaluate a forward/reverse primer pair against a template: Tm balance, clamp quality, primer-dimer ΔG, self-priming and amplicon check in one structured verdict.Molecular Beacon Judge — Evaluate molecular beacon designs: stem complementarity, loop length and Tm, loop-target fit, and whether the predicted fold matches the designed stem.Tm Mismatch Check — Evaluate oligo binding across mismatched or variant targets: per-target heteroduplex Tm, ΔG and melt-curve shifts for inclusivity and specificity.Pool Compatibility Check — Screen multiplex oligo pools for cross-dimer risk using pairwise thermodynamic free energy, not heuristic base-counting.ePCR Mapper — In-silico primer mapping across sequence databases to evaluate on-target and off-target amplicons with a confidence score.Primer Pair Designer — Design PCR primer pairs from a template and rank them by Tm, GC, hairpin ΔG, 3′ stability and dimer risk.Probe Designer — Design hydrolysis probes inside an amplicon and rank them by Tm, GC balance, hairpin stability and homopolymer risk.Learn — primer and probe design — Learn the thermodynamics and quality checks behind oligo design evaluation: melting temperature, hairpins, dimers, and design principles for primers and probes.Training Lab — Practice oligo design judgment with constraint puzzles built on real design rules.Community — Discuss oligo design, primer evaluation, and assay development with the OligoDesign community.Methods and citations — How OligoDesign evaluates oligo designs: published nearest-neighbor thermodynamic models, citations, validation against Primer3, and the OD Score behind every verdict.Contact — Get in touch with the OligoDesign team about oligo design evaluation tools.What is oligo design evaluation?
Built by Dr. Lifeng Lin, a bioinformatics scientist in nucleic acid assay development for in vitro
diagnostics since 2010. OligoDesign is a decision-support and educational tool; always independently
verify designs before synthesis or regulated use.