Classification and Structures of RNA

Nucleic acids have a primary, secondary, and tertiary structure analogous to the classification of protein structure. The sequence of bases in the nucleic acid chain gives the primary structure of DNA or RNA. The sequence of bases is read in a 5 -> 3 direction, so that you would read the structure in the next figure as ACGT. See Figure 8-1. 

It has become increasingly apparent that identification and classification of microorganisms can be enhanced by the vast genetic and structural information available in DNA, RNA, and protein sequences. Criteria based on sequences of ribosomal RNA (rRNA) genes have been used to... 

In the course of our examination of the morphogenesis and reproduction of viruses we shall follow the chemical principle of classification suggested by Cooper (1961), based on chemical structure of the genetic macromolecule of the virus (RNA, s ingle-stranded DNA, double-helical DNA) and their classification in accordance with the principal evolutionary groups (viruses of plants, of animals, and of bacteria). Viruses of bacteria are usually called bacteriophages. 

Pedersen, J. S., Bejerano, G., Siepel, A., et al. (2006) Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput. Biol. 2, e33. 

Other studies have focused on identifying surface residues that bind RNA. For example, this problem has been cast in the binary classification setting where the data comprises annotated structures gathered in a fashion similar to DNA-binding residue prediction these works have employed a number of classifiers including neural networks [48,49,52], SVM [53] and Naive Bayes [54]. This problem has also been cast in the structured-prediction setting, which is decomposed into a binary classification problem (solved by neural networks) followed by post-processing... 

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