Predictions of RNA secondary structure by combining homologous sequence information
1Mizuho Information & Research Institute, Inc, 2–3 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101–8443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2–41–6, Aomi, Koto-ku, Tokyo 135–0064, 3Department of Computational Intelligence and System Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226–8503, 4Japan Biological Informatics Consortium (JBIC), 2–45 Aomi, Koto-ku, Tokyo 135–8073 and 5Graduate School of Frontier Sciences, University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa 277–8562, Japan
*To whom correspondence should be addressed.
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Abstract |
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Motivation: Secondary structure prediction of RNA sequences is an important problem. There have been progresses in this area, but the accuracy of prediction from an RNA sequence is still limited. In many cases, however, homologous RNA sequences are available with the target RNA sequence whose secondary structure is to be predicted.
Results: In this article, we propose a new method for secondary structure predictions of individual RNA sequences by taking the information of their homologous sequences into account without assuming the common secondary structure of the entire sequences. The proposed method is based on posterior decoding techniques, which consider all the suboptimal secondary structures of the target and homologous sequences and all the suboptimal alignments between the target sequence and each of the homologous sequences. In our computational experiments, the proposed method provides better predictions than those performed only on the basis of the formation of individual RNA sequences and those performed by using methods for predicting the common secondary structure of the homologous sequences. Remarkably, we found that the common secondary predictions sometimes give worse predictions for the secondary structure of a target sequence than the predictions from the individual target sequence, while the proposed method always gives good predictions for the secondary structure of target sequences in all tested cases.
Availability: Supporting information and software are available online at: http://www.ncrna.org/software/centroidfold/ismb2009/.
Contact: hamada-michiaki{at}aist.go.jp
Supplementary information:Supplementary data are available at Bioinformatics online.
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