OPT: Codon optimize gene sequences for E. coli protein overexpression

• server evaluates likelihood gene sequences will express at a high level in E. coli. • server proposes synonymous gene sequences with greater probability of high expression. • method is based on a statistical model trained on 6000+ over-expression experiments. • OPT designs gave high yield for all eight commercial proteins tested. The ability to overexpress proteins is valuable for biotechnology, but not all sequences are compatible with high yield. We previously analyzed the sequence features and mRNA folding stability of a large data set of 6,384 distinct gene constructs, and developed a model for protein yield. Our OPT.williams.edu server (1) predicts the probability an input sequence will produce protein at a high level when overexpressed in E. coli , and (2) returns optimized synonymous sequences designed to boost protein expression. Here we also present experimental evidence of the high yields of our OPT constructs for eight commercially produced proteins.