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 as 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. For structure analysis, we show how to write feature filters that determine the presence of bulges, internal loops, hairpins, stem-loops, multibranches, and pseudoknots, along with their precise sizes. We additionally show use of ISO for high-throughput in silico screening of sequence variants used to architect new synthetic systems. ISO provides an easy mechanism to further understanding of structure-function relationships in natural systems, and to automate design tasks in synthetic systems.