CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure.

ABSTRACT

MOTIVATION An important problem in synthetic biology is to design a nucleotide sequence of an mRNA that confers a desirable expression level of a target protein. The secondary structure of protein-coding sequences (CDSs) is one potential factor that could have both positive and negative effects on protein production. To elucidate the role of secondary structure in CDSs, algorithms for manipulating secondary structure should be developed. RESULTS: We developed an algorithm for designing a CDS with the most stable secondary structure among all possible ones translated into the same protein, and implemented it as the program CDSfold. The algorithm runs the Zuker algorithm under the constraint of a given amino acid sequence. The time and space complexity is O(L(3)) and O(L(2)), respectively, where L is the length of the CDS to be designed. Although our algorithm is slower than the original Zuker algorithm, it could design a relatively long (2.7-kb) CDS in approximately 1 h. AVAILABILITY AND IMPLEMENTATION The CDSfold program is freely available for non-commercial users as stand-alone and web-based software from http//cdsfold.trahed.jp/cdsfold/ CONTACTS terai-goro@aist.go.jp or asai@k.u-tokyo.ac.jp SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.