title: An O(n(5)) algorithm for MFE prediction of kissing hairpins and 4-chains in nucleic acids.
abstract: Efficient methods for prediction of minimum free energy (MFE) nucleic secondary structures are widely used, both to better understand structure and function of biological RNAs and to design novel nano-structures. Here, we present a new algorithm for MFE secondary structure prediction, which significantly expands the class of structures that can be handled in O(n(5)) time. Our algorithm can handle H-type pseudoknotted structures, kissing hairpins, and chains of four overlapping stems, as well as nested substructures of these types.
authors.affiliation: Department of Electrical Engineering, California Institute of Technology, Pasadena, California, USA.
authors.forename: Ho-Lin
authors.initials: HL
authors.lastname: Chen
authors.forename: Anne
authors.initials: A
authors.lastname: Condon
authors.forename: Hosna
authors.initials: H
authors.lastname: Jabbari
mesh_terms: D000465:Algorithms; D052157:Aptamers, Nucleotide / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D052157:Aptamers, Nucleotide; D009696:Nucleic Acids