title: RNAfbinv: an interactive Java application for fragment-based design of RNA sequences.
abstract: CONCLUSIONS
  In RNA design problems, it is plausible to assume that the user would be interested in preserving a particular RNA secondary structure motif, or fragment, for biological reasons. The preservation could be in structure or sequence, or both. Thus, the inverse RNA folding problem could benefit from considering fragment constraints. We have developed a new interactive Java application called RNA fragment-based inverse that allows users to insert an RNA secondary structure in dot-bracket notation. It then performs sequence design that conforms to the shape of the input secondary structure, the specified thermodynamic stability, the specified mutational robustness and the user-selected fragment after shape decomposition. In this shape-based design approach, specific RNA structural motifs with known biological functions are strictly enforced, while others can possess more flexibility in their structure in favor of preserving physical attributes and additional constraints.
  
  
  BACKGROUND
  RNAfbinv is freely available for download on the web at http://www.cs.bgu.ac.il/~RNAexinv/RNAfbinv. The site contains a help file with an explanation regarding the exact use.
authors: Department of Computer Science, Ben Gurion University of the Negev, Beer Sheva 84105, Israel and Microsoft Research Israel, Herzliya 46733, Israel.
authors: Lina
authors: L
authors: Weinbrand
authors: Assaf
authors: A
authors: Avihoo
authors: Danny
authors: D
authors: Barash
mesh_terms: D020407:Internet; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D013816:Thermodynamics
chemical_list: D012313:RNA