Predictions of RNA secondary structure by combining homologous sequence information

Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai

Research output: Contribution to journalArticle

29 Citations (Scopus)

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 languageEnglish
JournalBioinformatics
Volume25
Issue number12
DOIs
Publication statusPublished - 2009
Externally publishedYes

Fingerprint

RNA Secondary Structure
Sequence Homology
RNA
Prediction
Secondary Structure
Target
Structure Prediction
Decoding
Computational Experiments

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 journalArticle

Hamada, Michiaki ; Sato, Kengo ; Kiryu, Hisanori ; Mituyama, Toutai ; Asai, Kiyoshi. / Predictions of RNA secondary structure by combining homologous sequence information. In: Bioinformatics. 2009 ; Vol. 25, No. 12.
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