An O(n5) algorithm for MFE prediction of kissing hairpins and 4-chains in nucleic acids
Journal
Journal of Computational Biology
Journal Volume
16
Journal Issue
6
Pages
803-815
Date Issued
2009
Author(s)
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.
SDGs
Type
journal article