Comparative Analysis of the Higher-Order Structure of RNA
“If you want to understand function, study structure”
The functions of many RNA molecules are directly associated with their higher-order structure, and given the vast abundance of their functions in a cell, the determination of their structures should contribute significantly to our understanding of the cell. A variety of methods are used to determine their higher-order structure. A multitude of experimental methods are discussed elsewhere in this book. Computational methods are also used. The first type, considered one of the grand challenges in biology, utilizes different fundamental principles of RNA structure to predict their secondary and three-dimensional structure. While the accuracies of these methods have been improving, generally speaking, higher-quality structure information is obtained with experimental methods. In contrast to the computational methods that utilize first principles to predict the RNA’s higher-order structure, comparative methods are utilized to infer structure, function, and evolution from the patterns of sequence and structure conservation and variation. The primary objective of this chapter is to briefly review the use of comparative analysis to deduce information about RNA structure, using an evolutionary framework.
KeywordsRNA structure Computational comparative analysis RNA structure motifs Covariation analysis
The author appreciates the funding from the National Institutes of Health (GM067317) and the Welch Foundation (F-1427) to support the research in the Gutell lab.
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