RNAiFold2T: Constraint Programming design of thermo-IRES switches.

ABSTRACT:

Motivation

RNA thermometers (RNATs) are cis-regulatory elements 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 first 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 soluti

SUBMITTER: Garcia-Martin JA 

PROVIDER: S-EPMC4908349 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature