RNAiFold

RNAiFold is a unique software tool that allows for designing RNA molecules with a specific target structure. Unlike other approaches using heuristic methods, RNAiFold uses exhaustive constraint programming to generate all possible sequences that fold into the target RNA structure or determine no solution. This feature makes RNAiFold an efficient and reliable tool for designing synthetic constructs, such as riboswitches, ribozymes, and thermoswitches.

RNAiFold 2.0 is a complete overhaul of the previous version, RNAiFold 1.0, which was written in the now-defunct COMET language. The new version is written in C++, which has made it more efficient and user-friendly. The software now includes a user-friendly pipeline that allows users to design synthetic constructs with the functionality of given Rfam families. This new feature has extended the capabilities of RNAiFold 2.0, making it more versatile and adaptable to different applications.

One of the most significant upgrades in RNAiFold 2.0 is its support for amino acid constraints, even for proteins translated in different reading frames from overlapping coding sequences. This feature has expanded the scope of RNAiFold 2.0, making it possible to design more complex RNA molecules with specific amino acid sequences. Additionally, the new software has expanded its structure compatibility and incompatibility constraints, allowing for the design of single RNA molecules and hybridization complexes of two RNA molecules.