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The detection and assessment of possible RNA secondary structure using multiple sequence alignment

Published: 11 March 2007 Publication History

Abstract

We here devise a new method for detecting and assessing RNA secondary structure by using multiple sequence alignment. The central idea of the method is to first detect conserved stems in the alignment using a special matrix and then assess them by evaluating the ratio of the signal to the noise. We tested the method on data sets composed of pairwise and three-way alignments of known ncRNAs. For the pairwise tests, our method has sensitivity 61.42% and specificity 97.05% for structural alignments, and sensitivity 42.05% and specificity 98.15% for BLAST alignments. For the three-way tests, our method has sensitivity 65.17% and specificity 97.96% for structural alignments, and sensitivity 40.70% and specificity 97.87% for CLUSTALW alignments. Our method can detect conserved secondary structures in gapped or ungapped RNA alignments.

References

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Bernardo, D. d., Down, T. et al. ddbRNA: detection of conserved secondary structures in multiple alignments. Bioinformatics, 19(13): 1606--1611, 2003.
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Durbin, R., Eddy, S. et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge, Cambridge University press, pp.46--79, 1998.
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Hofacker, I., Fekete, M. et al. Secondary structure prediction for aligned RNA sequences. Journal of Molecular Biology, 319(5): 1059--1066, 2002.
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Huttenhofer, A., Schattner, P. et al. Non-coding RNAs:hope or hype? TRENDS in Genetics, 21(5): 289--297, 2005.
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Knudsen, B. and Hein, J. Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Research, 31(13): 3423--3428, 2003.
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Mathews, D. and Turner, D. Dynalign: An algorithm for finding the secondary structure common to two RNA sequences. Journal of Molecular Biology, 317(2): 191--203, 2002.
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Sam, G. J., Simon, M. et al. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Research, 33(Supplement 1): D121--D124, 2005.
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Cited By

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  • (2008)Predicting RNA secondary structure using profile stochastic context-free grammars and phylogenic analysisJournal of Computer Science and Technology10.1007/s11390-008-9154-723:4(582-589)Online publication date: 1-Jul-2008
  • (2007)Constructing structural alignment of RNA sequences by detecting and assessing conserved stemsProceedings of the 2007 international conference on Life System Modeling and Simulation10.5555/2393672.2393699(208-217)Online publication date: 14-Sep-2007
  • (2007)The Prediction of RNA Secondary Structure Using Multiple Unaligned SequencesProceedings of the Third International Conference on Natural Computation - Volume 0210.1109/ICNC.2007.733(367-374)Online publication date: 24-Aug-2007

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  1. The detection and assessment of possible RNA secondary structure using multiple sequence alignment

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        cover image ACM Conferences
        SAC '07: Proceedings of the 2007 ACM symposium on Applied computing
        March 2007
        1688 pages
        ISBN:1595934804
        DOI:10.1145/1244002
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        Publication History

        Published: 11 March 2007

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        Author Tags

        1. RNA secondary structure
        2. multiple sequence alignment
        3. non-coding RNA

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        View all
        • (2008)Predicting RNA secondary structure using profile stochastic context-free grammars and phylogenic analysisJournal of Computer Science and Technology10.1007/s11390-008-9154-723:4(582-589)Online publication date: 1-Jul-2008
        • (2007)Constructing structural alignment of RNA sequences by detecting and assessing conserved stemsProceedings of the 2007 international conference on Life System Modeling and Simulation10.5555/2393672.2393699(208-217)Online publication date: 14-Sep-2007
        • (2007)The Prediction of RNA Secondary Structure Using Multiple Unaligned SequencesProceedings of the Third International Conference on Natural Computation - Volume 0210.1109/ICNC.2007.733(367-374)Online publication date: 24-Aug-2007

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