title: Novel representation of RNA secondary structure used to improve prediction algorithms.
abstract: We propose a novel representation of RNA secondary  structure for a quick comparison of different structures. Secondary structure  was viewed as a set of stems and each stem was represented by two values  according to its position. Using this representation, we improved the  comparative sequence analysis method results and the minimum free-energy model.  In the comparative sequence analysis method, a novel algorithm independent of  multiple sequence alignment was developed to improve performance. When dealing  with a single-RNA sequence, the minimum free-energy model is improved by  combining it with RNA class information. Secondary structure prediction  experiments were done on tRNA and RNAse P RNA; sensitivity and specificity were  both improved. Furthermore, software programs were developed for non-commercial  use.
authors.affiliation: School of Information Science and Technology, Xiamen University, Xiamen, China.
authors.forename: Q
authors.initials: Q
authors.lastname: Zou
authors.forename: C
authors.initials: C
authors.lastname: Lin
authors.forename: X-Y
authors.initials: XY
authors.lastname: Liu
authors.forename: Y-P
authors.initials: YP
authors.lastname: Han
authors.forename: W-B
authors.initials: WB
authors.lastname: Li
authors.forename: M-Z
authors.initials: MZ
authors.lastname: Guo
mesh_terms: D000465:Algorithms; D042322:Anaplasma marginale / Q000235:genetics; D001483:Base Sequence; D006217:Halobacterium / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010963:Plasmodium falciparum / Q000235:genetics; D019642:RNA, Archaeal / Q000737:chemistry*; D012329:RNA, Bacterial / Q000737:chemistry*; D016053:RNA, Protozoan / Q000737:chemistry*; D012343:RNA, Transfer / Q000737:chemistry*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods; D013816:Thermodynamics
chemical_list: D019642:RNA, Archaeal; D012329:RNA, Bacterial; D016053:RNA, Protozoan; D012343:RNA, Transfer