PAIRDesign

Coding-sequence design on measured codon-pair half-life and RNA structure, from the Giraldez Lab at Yale University.

If you use this tool, please cite Lee, H., Musaev, D., Vejnar, C.E., Krishna, S., Nguyen, T.D., Strayer, E.C., Abdel Messih, M., Takacs, C.M., Beaudoin, J.-D., and Giraldez, A.J. (2026). Beyond codon optimality: codon pairs regulate mRNA stability dependent on translation. bioRxiv.

Design a coding sequence

Spaces, digits and line breaks are ignored.
Folding energy is evaluated at the species' temperature.
Minimises ΔG − λ × Σ pair half-life. Higher λ favours half-life.
starting…
0 s elapsed

Designs

How it works

The PAIRDesign is the joint optimization of codon-pair context and RNA secondary structure for stable mRNA engineering. This webite provides beam=500 and the local search algorithm for faster optimization. The optimum of both codon pair stability and RNA structure is accessible on PAIRDesign. The λ=0 is the structure-only optimum, and λ=∞ is the codon-pair-only optimum.

© Giraldez Lab — Yale
PAIRDesign