swMATH ID: 15050
Software Authors: Juan Antonio Garcia-Martin, Ivan Dotu, Javier Fernandez-Chamorro, Gloria Lozano, Jorge Ramajo, Encarnacion Martinez-Salas, Peter Clote
Description: RNAiFold2T: Constraint Programming design of thermo-IRES switches. Motivation: RNA thermometers (RNATs) are cis-regulatory ele- ments that change secondary structure upon temperature shift. Often involved in the regulation of heat shock, cold shock and virulence genes, RNATs constitute an interesting potential resource in synthetic biology, where engineered RNATs could prove to be useful tools in biosensors and conditional gene regulation. Results: Solving the 2-temperature inverse folding problem is critical for RNAT engineering. Here we introduce RNAiFold2T, the ?rst Constraint Programming (CP) and Large Neighborhood Search (LNS) algorithms to solve this problem. Benchmarking tests of RNAiFold2T against existent programs (adaptive walk and genetic algorithm) inverse folding show that our software generates two orders of magnitude more solutions, thus allow- ing ample exploration of the space of solutions. Subsequently, solutions can be prioritized by computing various measures, including probability of target structure in the ensemble, melting temperature, etc. Using this strategy, we rationally designed two thermosensor internal ribosome entry site (thermo-IRES) elements, whose normalized cap-independent transla- tion e?ciency is approximately 50
Homepage: http://bioinformatics.bc.edu/clotelab/RNAiFold/
Dependencies: ViennaRNA
Cited in: 0 Publications