An O(n(5)) algorithm for MFE prediction of kissing hairpins and 4-chains in nucleic acids.
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.
Chen
Ho-Lin
HL
Department of Electrical Engineering, California Institute of Technology, Pasadena, California, USA.
Condon
Anne
A
Jabbari
Hosna
H
D000465:Algorithms; D052157:Aptamers, Nucleotide / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D013816:Thermodynamics
D052157:Aptamers, Nucleotide; D009696:Nucleic Acids