title: Dynamic programming algorithms for RNA structure prediction with binding sites.
abstract: Noncoding antisense RNAs have recently occupied considerable attention and several computational studies have been made on RNA-RNA interaction prediction. In this paper, we present novel dynamic programming algorithms for predicting the minimum energy secondary structure when binding sites of one of the two interacting RNAs are known. Experimental results on several known RNA-RNA interaction data show that our proposed method achieves good performance in accuracy and time.
authors.affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan. unyanee@kuicr.kyoto-u.ac.jp
authors.forename: Unyanee
authors.initials: U
authors.lastname: Poolsap
authors.forename: Yuki
authors.initials: Y
authors.lastname: Kato
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Akutsu
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D019295:Computational Biology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D016372:RNA, Antisense / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D016372:RNA, Antisense; D012329:RNA, Bacterial; D022661:RNA, Untranslated; D012313:RNA