I'm trying to optimize Streptococcus pyrogenes cas9 sequence (ca. 4000nt) for expression in maize.
GeneGA package seems optimal (command GeneGA, optimalizing both codon bias and mRNA secondary structure) but it has poor documentation. I've created custom CAI table. After ca. four days of analysis I've got sequence with approximately -1000 free energy, and plots shows rather sinusoidal trends than convergence.
Are here somebody who have used this package and could share knowledge about good program options for long RNAs? Vignette just states that "longer region needs larger popSize and iters".
Has anybody care about secondary structure? It seems that it is inevitable.