Mining frequent stem patterns from unaligned RNA sequences

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

Research output: Contribution to journalArticle

35 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)2480-2487
Number of pages8
JournalBioinformatics
Volume22
Issue number20
DOIs
Publication statusPublished - 2006 Oct
Externally publishedYes

Fingerprint

RNA
Mining
Secondary Structure
Untranslated RNA
Graph Mining
Structure Prediction
Graph in graph theory
Necessary

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

Mining frequent stem patterns from unaligned RNA sequences. / Hamada, Michiaki; Tsuda, Koji; Kudo, Taku; Kin, Taishin; Asai, Kiyoshi.

In: Bioinformatics, Vol. 22, No. 20, 10.2006, p. 2480-2487.

Research output: Contribution to journalArticle

Hamada, Michiaki ; Tsuda, Koji ; Kudo, Taku ; Kin, Taishin ; Asai, Kiyoshi. / Mining frequent stem patterns from unaligned RNA sequences. In: Bioinformatics. 2006 ; Vol. 22, No. 20. pp. 2480-2487.
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