mRNA vaccine design

[wangjiawen2013]

Hi,
DnaChisel is a tool for DNA optimisation, is it suitable for mRNA design ? We want develop an mRNA vaccine, so we need to optimize the mRNA sequence. Lineardesign(https://github.com/LinearDesignSoftware/LinearDesign) is specific to mRNA design, what's the core difference between DnaChisel and Lineardesign in mRNA sequence design?

[Zulko]

This is an old issue but in case it is still useful: DnaChisel can be used for mRNA design, see this project from Merck where they combine DnaChisel and ViennaRNA, or mRNArchitect for another example.

LinearDesign focuses on mRNA structure (to create or remove secondary structures) while DnaChisel focuses on multi-constrain optimization: it optimizes secondary structure along with codon usage, manufacturer constraints, etc. One strategy could be to combine the two frameworks, for instance optimizing the sequence with LinearDesign first, then with DnaChisel.