Mining frequent stem patterns from unaligned RNA sequences

Michiaki Hamada*, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai

*この研究の対応する著者

研究成果: Article査読

36 被引用数 (Scopus)

抄録

Motivation: In detection of non-coding RNAs, it is often necessary to identify the secondary structure motifs from a set of putative RNA sequences. Most of the existing algorithms aim to provide the best motif or few good motifs, but biologists often need to inspect all the possible motifs thoroughly. Results: Our method RNAmine employs a graph theoretic representation of RNA sequences and detects all the possible motifs exhaustively using a graph mining algorithm. The motif detection problem boils down to finding frequently appearing patterns in a set of directed and labeled graphs. In the tasks of common secondary structure prediction and local motif detection from long sequences, our method performed favorably both in accuracy and in efficiency with the state-of-the-art methods such as CMFinder.

本文言語English
ページ(範囲)2480-2487
ページ数8
ジャーナルBioinformatics
22
20
DOI
出版ステータスPublished - 2006 10月
外部発表はい

ASJC Scopus subject areas

  • 統計学および確率
  • 生化学
  • 分子生物学
  • コンピュータ サイエンスの応用
  • 計算理論と計算数学
  • 計算数学

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