SwiftLib: rapid degenerate-codon-library optimization through dynamic programming.

ABSTRACT: Degenerate codon (DC) libraries efficiently address the experimental library-size limitations of directed evolution by focusing diversity toward the positions and toward the amino acids (AAs) that are most likely to generate hits; however, manually constructing DC libraries is challenging, error prone and time consuming. This paper provides a dynamic programming solution to the task of finding the best DCs while keeping the size of the library beneath some given limit, improving on the existing integer-linear programming formulation. It then extends the algorithm to consider multiple DCs at each position, a heretofore unsolved problem, while adhering to a constraint on the number of primers needed to synthesize the library. In the two library-design problems examined here, the use of multi

SUBMITTER: Jacobs TM 

PROVIDER: S-EPMC4357694 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature