Codon Adaptation Index
Resistance to RNAi of the original gene (achieving the requested CAI might not be possible in all cases)
Ensures that for each series of 21 nucleotides, the optimized construct differs from the original gene in atleast two codons.
Optimize for weak mRNA structure at ribosome binding site (nucleotides -4 to +37)
Minimizes the energy needed to unfold the ribosome binding site.
Avoid splice sites in coding region (may result in a CAI lower than specified)
Optimization can sometimes lead to the introduction of artifical splice sites. Enabling this option will result in the prediction of potential splice sites and their removal.
Codon adaptation-based control of protein expression in C. elegans.
Redemann S, Schloissnig S, Ernst S, Pozniakowsky A, Ayloo S, Hyman AA, Bringmann H.
2011 Mar;8(3):250-2. Epub 2011 Jan 30.
schloi (at) mpi-cbg (dot) de