title: incaRNAfbinv: a web server for the fragment-based design of RNA sequences.
abstract: In recent years, new methods for computational RNA design have been developed and applied to various problems in synthetic biology and nanotechnology. Lately, there is considerable interest in incorporating essential biological information when solving the inverse RNA folding problem. Correspondingly, RNAfbinv aims at including biologically meaningful constraints and is the only program to-date that performs a fragment-based design of RNA sequences. In doing so it allows the design of sequences that do not necessarily exactly fold into the target, as long as the overall coarse-grained tree graph shape is preserved. Augmented by the weighted sampling algorithm of incaRNAtion, our web server called incaRNAfbinv implements the method devised in RNAfbinv and offers an interactive environment for the inverse folding of RNA using a fragment-based design approach. It takes as input: a target RNA secondary structure; optional sequence and motif constraints; optional target minimum free energy, neutrality and GC content. In addition to the design of synthetic regulatory sequences, it can be used as a pre-processing step for the detection of novel natural occurring RNAs. The two complementary methodologies RNAfbinv and incaRNAtion are merged together and fully implemented in our web server incaRNAfbinv, available at http://www.cs.bgu.ac.il/incaRNAfbinv.
authors.affiliation: Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel.
authors.forename: Matan
authors.initials: M
authors.lastname: Drory Retwitzer
authors.affiliation: School of Computer Science & McGill Centre for Bioinformatics, McGill University, Montréal, QC H3A 0E9, Canada.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Reinharz
authors.affiliation: Laboratoire d'Informatique (LIX)-CNRS UMR 7161, École Polytechnique, 91128 Palaiseau, France AMIB team/project, INRIA Saclay, Bâtiment Alan Turing, 91128 Palaiseau, France.
authors.forename: Yann
authors.initials: Y
authors.lastname: Ponty
authors.affiliation: School of Computer Science & McGill Centre for Bioinformatics, McGill University, Montréal, QC H3A 0E9, Canada.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Waldispühl
authors.affiliation: Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel dbarash@cs.bgu.ac.il.
authors.forename: Danny
authors.initials: D
authors.lastname: Barash
mesh_terms: D000465:Algorithms; D001482:Base Composition; D020029:Base Pairing; D001483:Base Sequence; D003196:Computer Graphics; D020407:Internet; D009154:Mutation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D059370:RNA Folding; D017423:Sequence Analysis, RNA; D012984:Software; D013816:Thermodynamics
chemical_list: D012313:RNA