ISO: Numeric Representation of Nucleic Acid Form

We report a representation, ISO, that unambiguously and compactly describes patterns in nucleic acid secondary structure. ISO is equally expressive as other methodologies including dot-parenthesis notation, and various structure graph variations, for representation of well-formed structure patterns. ISO naturally expresses pseudoknot structures as well, without a change or extension in notation, an advantage not possible with commonly used representations. The numerical basis of ISO is readily amenable to development of mathematical evaluation rules, distance metrics, and further abstraction for either design or analysis purposes. In this way, ISO provides an easy mechanism for high-throughput in silico screening of sequence variants for architecting new synthetic systems, and better understanding of structure-function relationships and structure space in natural systems.

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ACM Conference on Bioinformatics, Computational Biology and Biomedicine