title: RNAiFold: a web server for RNA inverse folding and molecular design.
abstract: Synthetic biology and nanotechnology are poised to make revolutionary contributions to the 21st century. In this article, we describe a new web server to support in silico RNA molecular design. Given an input target RNA secondary structure, together with optional constraints, such as requiring GC-content to lie within a certain range, requiring the number of strong (GC), weak (AU) and wobble (GU) base pairs to lie in a certain range, the RNAiFold web server determines one or more RNA sequences, whose minimum free-energy secondary structure is the target structure. RNAiFold provides access to two servers: RNA-CPdesign, which applies constraint programming, and RNA-LNSdesign, which applies the large neighborhood search heuristic; hence, it is suitable for larger input structures. Both servers can also solve the RNA inverse hybridization problem, i.e. given a representation of the desired hybridization structure, RNAiFold returns two sequences, whose minimum free-energy hybridization is the input target structure. The web server is publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold, which provides access to two specialized servers: RNA-CPdesign and RNA-LNSdesign. Source code for the underlying algorithms, implemented in COMET and supported on linux, can be downloaded at the server website.
authors.affiliation: Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Garcia-Martin
authors.forename: Peter
authors.initials: P
authors.lastname: Clote
authors.forename: Ivan
authors.initials: I
authors.lastname: Dotu
mesh_terms: D000465:Algorithms; D001482:Base Composition; D020029:Base Pairing; D001483:Base Sequence; D003198:Computer Simulation; D020407:Internet; D012313:RNA / Q000737:chemistry; D059370:RNA Folding; D012984:Software
chemical_list: D012313:RNA