CentroidHomfold-LAST: Accurate prediction of RNA secondary structure using automatically collected homologous sequences

Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C. Frith, Kiyoshi Asai

研究成果: Article査読

15 被引用数 (Scopus)

抄録

Although secondary structure predictions of an individual RNA sequence have been widely used in a number of sequence analyses of RNAs, accuracy is still limited. Recently, we proposed a method (called 'CentroidHomfold'), which includes information about homologous sequences into the prediction of the secondary structure of the target sequence, and showed that it substantially improved the performance of secondary structure predictions. CentroidHomfold, however, forces users to prepare homologous sequences of the target sequence. We have developed a Web application (CentroidHomfold-LAST) that predicts the secondary structure of the target sequence using automatically collected homologous sequences. LAST, which is a fast and sensitive local aligner, and CentroidHomfold are employed in the Web application. Computational experiments with a commonly-used data set indicated that CentroidHomfold-LAST substantially outperformed conventional secondary structure predictions including CentroidFold and RNAfold.

本文言語English
ページ(範囲)W100-W106
ジャーナルNucleic acids research
39
SUPPL. 2
DOI
出版ステータスPublished - 2011 7 1
外部発表はい

ASJC Scopus subject areas

  • Genetics

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