RNAiFold: A constraint programming algorithm for RNA inverse folding and molecular design
Synthetic biology currently is a rapidly emerging discipline, where innovative and interdisciplinary work has led to promising results. Synthetic design of RNA requires novel methods for the study and analysis of known functional molecules, as well as to generate design candidates that have a high likelihood of being functional. In particular, RNA inverse folding (finding a RNA sequence which folds into a given target structure) has been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding in that (exhaustive) constraint programming is used instead of heuristic methods.
Constraint programming, often used to face NP-complete problems, allows the design efficient software based on a clean and comprehensible model. RNAiFold supports a wide range of design constraints, such as sequence constraints, amino acid constraints, even for proteins translated in different reading frames from overlapping coding sequences; structure compatibility/incompatibility constraints and control GC content. With these features, RNAiFold allows the user to design single RNA molecules as well as hybridization complexes of two RNA molecules and has been successfully applied to functional RNA element discovery and synthetic design of ribozymes.
Bio: Juan Antonio Garcia is a Ph.D. student at Boston College.