title: Cofolga: a genetic algorithm for finding the common folding of two RNAs.
abstract: In order to predict non-coding RNA genes and functions on the basis of genome sequences, accurate secondary structure prediction is useful. Although single-sequence folding programs such as mfold have been successful, it is of great importance to develop a novel approach for further improvement of the prediction performance. In the present paper, a secondary structure prediction method based on genetic algorithm, Cofolga, is proposed. The program developed performs folding and alignment of two homologous RNAs simultaneously. Cofolga was tested with a dataset composed of 13 tRNAs, seven 5S rRNAs, five RNase P RNAs, and five SRP RNAs; as a result, it turned out that the average prediction accuracies for the tRNAs, 5S rRNAs, RNase P RNAs, and SRP RNAs obtained by Cofolga with an optimal weight factor and default parameters were 83.6, 81.8, 73.5, and 67.7%, respectively. These results were superior to those obtained by a single-sequence folding based on free-energy minimization in which corresponding average prediction accuracies were 52.4, 47.4, 57.7, and 52.3%, respectively. Cofolga has a post-processing in which a single-sequence folding is performed after fixation of a predicted common structure; this post-processing enables Cofolga to predict a structure that is present in one of two RNAs alone. The executable files of Cofolga (for Windows/Unix/Mac) can be obtained by an e-mail request.
authors.affiliation: Department of Electronic and Information System Engineering, Faculty of Science and Technology, Hirosaki University, Hirosaki 036-8561, Japan. taneda@si.hirosaki-u.ac.jp
authors.forename: Akito
authors.initials: A
authors.lastname: Taneda
mesh_terms: D000465:Algorithms; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012341:RNA, Ribosomal, 5S / Q000737:chemistry*; D012343:RNA, Transfer / Q000737:chemistry*; D043262:Ribonuclease P / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D018271:Signal Recognition Particle / Q000235:genetics; D013816:Thermodynamics
chemical_list: D012341:RNA, Ribosomal, 5S; C490326:SRP14 protein, human; D018271:Signal Recognition Particle; D012343:RNA, Transfer; D043262:Ribonuclease P