Bioinformatics Advance Access originally published online on August 14, 2006
Bioinformatics 2006 22(20):2480-2487; doi:10.1093/bioinformatics/btl431
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Mining frequent stem patterns from unaligned RNA sequences
1 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST) 2-43 Aomi, Koto-ku, Tokyo, Japan
2 Mizuho Information & Research Institute, Inc. 2-3, Kanda-Nishikicho, Chiyoda-ku, Tokyo 101-8443, Japan
3 Department of Computational Intelligence and System Science, Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
4 Max Planck Institute for Biological Cybernetics Spemannstr. 38, 72076 Tubingen, Germany
5 Google Japan, Inc., 26-1, Sakuracho, Shibuya Tokyo 150-8512, Japan
6 Graduate School of Frontier Sciences, University of Tokyo 5-1-5, Kashiwanoha, Kashiwa, Chiba 277–8562, Japan
*To whom correspondence should be addressed.
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.
Availability: The software is available upon request.
Contact: hamada-michiaki{at}aist.go.jp
Supplementary information: Visit the following URL for Supplementary information, software availability and the information about the web server: http://www.ncrna.org/RNAMINE/
Received on May 12, 2006; revised on July 26, 2006; accepted on August 3, 2006
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