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Cardioviral RNA structure logo analysis: entropy, correlations, and prediction

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Abstract

In recent years, there has been an increased number of sequenced RNAs leading to the development of new RNA databases. Thus, predicting RNA structure from multiple alignments is an important issue to understand its function. Since RNA secondary structures are often conserved in evolution, developing methods to identify covariate sites in an alignment can be essential for discovering structural elements. Structure Logo is a technique established on the basis of entropy and mutual information measured to analyze RNA sequences from an alignment. We proposed an efficient Structure Logo approach to analyze conservations and correlations in a set of Cardioviral RNA sequences. The entropy and mutual information content were measured to examine the conservations and correlations, respectively. The conserved secondary structure motifs were predicted on the basis of the conservation and correlation analyses. Our predictive motifs were similar to the ones observed in the viral RNA structure database, and the correlations between bases also corresponded to the secondary structure in the database.

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Authors and Affiliations

  1. Modern Biology Research Center, Yunnan University, Kunming, 650091, China

    Xiao-Zhou Chen, Huai Cao & Ci-Quan Liu

  2. School of Mathematics and Computer Science, Yunnan Nationalities University, Kunming, 650031, China

    Xiao-Zhou Chen

  3. Department of Cell Biology and Genetics, Kunming Medical College, Kunming, 650031, China

    Wen Zhang

  4. Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China

    Ci-Quan Liu

  5. Theotetical Biology Research Center, Peking University, Beijing, 100871, China

    Ci-Quan Liu

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  1. Xiao-Zhou Chen
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  2. Huai Cao
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  3. Wen Zhang
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  4. Ci-Quan Liu
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Corresponding author

Correspondence to Ci-Quan Liu.

Additional information

This work was partly supported by NSFC (Natural Science Foundation of China, Nos. 90303018 and 90208018). We thank the referees for help.

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Chen, XZ., Cao, H., Zhang, W. et al. Cardioviral RNA structure logo analysis: entropy, correlations, and prediction. J Biol Phys 36, 145–159 (2010). https://doi.org/10.1007/s10867-009-9154-z

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  • DOI: https://doi.org/10.1007/s10867-009-9154-z

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