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Spectrum-like graphical representation of RNA secondary structure

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Abstract

We consider graphical representation for RNA secondary structure by assigning four horizontal lines to the unpaired bases A, C, G, U and four horizontal lines to paired bases A′, C′, G′, U′. The RNA graphical representation based on eight equidistant horizontal lines can be viewed as natural extension of the earlier four-line graphical representation of DNA (Randić et al., Chem Phys Lett, 2003, 371, 202) to RNA. Numerical characterization of RNA is based on 8 × 8 matrices recording the adjacency of the nucleotide bases in the primary sequence of RNA when RNA is read from 5′ to 3′. The approach is illustrated on a set of nine viral RNAs, reported in the literature. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009

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