title: RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.
abstract: Several algorithms for RNA inverse folding have 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. For that reason, RNAiFold can generate all sequences that fold into the target structure or determine that there is no solution. RNAiFold 2.0 is a complete overhaul of RNAiFold 1.0, rewritten from the now defunct COMET language to C++. The new code properly extends the capabilities of its predecessor by providing a user-friendly pipeline to design synthetic constructs having the functionality of given Rfam families. In addition, the new software supports amino acid constraints, even for proteins translated in different reading frames from overlapping coding sequences; moreover, structure compatibility/incompatibility constraints have been expanded. With these features, RNAiFold 2.0 allows the user to design single RNA molecules as well as hybridization complexes of two RNA molecules.
  
  
  BACKGROUND
  the web server, source code and linux binaries are publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold2.0.
authors.affiliation: Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA.
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Garcia-Martin
authors.affiliation: Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute); C/Dr. Aiguader 88, Barcelona E-08003, Spain.
authors.forename: Ivan
authors.initials: I
authors.lastname: Dotu
authors.affiliation: Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA clote@bc.edu.
authors.forename: Peter
authors.initials: P
authors.lastname: Clote
mesh_terms: D000465:Algorithms; D020407:Internet; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding; D020539:Sequence Analysis, Protein; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D012313:RNA