Folding 3-noncrossing RNA pseudoknot structures.
In this article, we present the novel ab initio folding algorithm cross, which generates minimum free energy (mfe), 3-noncrossing, canonical RNA structures. Here an RNA structure is 3-noncrossing if it does not contain three or more mutually crossing arcs and canonical, if each of its stacks has size greater or equal than two. Our notion of mfe-structure is based on a specific concept of pseudoknots and respective loop-based energy parameters. The algorithm decomposes into three subroutines: first the inductive construction of motifs and their associated shadows, second the generation of the (rooted) skeleta-trees and third the saturation of the skeleta via context dependent dynamic programming routines.
Huang
Fenix W D
FW
Center for Combinatorics, LPMC-TJKLC, Tianjin, PR China.
Peng
Wade W J
WW
Reidys
Christian M
CM
D000465:Algorithms; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012343:RNA, Transfer / Q000737:chemistry; D038621:Regulatory Sequences, Ribonucleic Acid / Q000235:genetics
D038621:Regulatory Sequences, Ribonucleic Acid; D012313:RNA; D012343:RNA, Transfer