Cofolga: a genetic algorithm for finding the common folding of two RNAs. 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 a 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.
Keywords for this software
References in zbMATH (referenced in 2 articles , 1 standard article )
Showing results 1 to 2 of 2.
- Machado-Lima, Ariane; del Portillo, Hernando A.; Durham, Alan Mitchell: Computational methods in noncoding RNA research (2008)
- Taneda, Akito: Cofolga: a genetic algorithm for finding the common folding of two RNAs (2005)