Bacterial Regulatory RNA pp 99-122

Part of the Methods in Molecular Biology book series (MIMB, volume 905)

RNA Structure Prediction: An Overview of Methods


RNA is now appreciated to serve numerous cellular roles, and understanding RNA structure is important for understanding a mechanism of action. This contribution discusses the methods available for predicting RNA structure. Secondary structure is the set of the canonical base pairs, and secondary structure can be accurately determined by comparative sequence analysis. Secondary structure can also be predicted. The most commonly used method is free energy minimization. The accuracy of structure prediction is improved either by using experimental mapping data or by predicting a structure conserved in a set of homologous sequences. Additionally, tertiary structure, the three-dimensional arrangement of atoms, can be modeled with guidance from comparative analysis and experimental techniques. New approaches are also available for predicting tertiary structure.

Key words

Statistical mechanics Comparative sequence analysis Gibbs free energy Dynamic programming algorithm RNA secondary structure 


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© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of Biochemistry & BiophysicsUniversity of Rochester Medical CenterRochesterUSA
  2. 2.Department of Biochemistry & Biophysics, Center for RNA BiologyUniversity of Rochester Medical CenterRochesterUSA
  3. 3.Department of Biostatistics & Computational BiologyUniversity of Rochester Medical CenterRochesterUSA

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