Abstract
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.
| Original language | English |
|---|---|
| Journal | Bioinformatics |
| Volume | 25 |
| Issue number | 12 |
| DOIs | |
| Publication status | Published - 2009 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Biochemistry
- Molecular Biology
- Computational Theory and Mathematics
- Computer Science Applications
- Computational Mathematics
- Statistics and Probability
Cite this
Predictions of RNA secondary structure by combining homologous sequence information. / Hamada, Michiaki; Sato, Kengo; Kiryu, Hisanori; Mituyama, Toutai; Asai, Kiyoshi.
In: Bioinformatics, Vol. 25, No. 12, 2009.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Predictions of RNA secondary structure by combining homologous sequence information
AU - Hamada, Michiaki
AU - Sato, Kengo
AU - Kiryu, Hisanori
AU - Mituyama, Toutai
AU - Asai, Kiyoshi
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
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U2 - 10.1093/bioinformatics/btp228
DO - 10.1093/bioinformatics/btp228
M3 - Article
VL - 25
JO - Bioinformatics
JF - Bioinformatics
SN - 1367-4803
IS - 12
ER -