What are the good tools for mRNA codon usage optimization and secondary structure prediction?

Question

[jack]

Hi all,

I'm looking for tool to do codon usage optimization for mRNAs and secondary structure prediction;

Basically I need to optimize codon usage to increase expression of the gene in host cell. Also I need to confirm that in the new sequence ribosome binding site are exposed and it's not involved in any secondary structure.

Would someone recommend some tools?

Answer 1

[Asaf]

You can use RNAup for your second task, it gives an accessibility value for each window.