ISO: numeric representation of nucleic acid form

M L Fanning; Joanne Macdonald; D Stefanovic

doi:10.1145/2147805.2147859

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ISO: numeric representation of nucleic acid form

Conference paper

Peer reviewed

ISO: numeric representation of nucleic acid form

M L Fanning, Joanne Macdonald and D Stefanovic

Proceedings of the 2nd Association for Computer Machinery Conference on Bioinformatics, Computational Biology and Biomedicine, pp.404-408

Association for Computer Machinery (ACM) International Conference on Bioinformatics, Computational Biology and Biomedicine (BCB' 11), 2011 (Chicago, United States, 31-Jul-2011–03-Aug-2011)

Association for Computer Machinery

2011

DOI: https://doi.org/10.1145/2147805.2147859

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Abstract

Biochemistry and Cell Biology

algorithms

design

performance

standardization

verification

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.

Details

Title: ISO: numeric representation of nucleic acid form
Authors: M L Fanning (Author) - University of New Mexico, United States
Joanne Macdonald (Author) - University of Columbia, United States
D Stefanovic (Author) - University of New Mexico, United States
Publication details: Proceedings of the 2nd Association for Computer Machinery Conference on Bioinformatics, Computational Biology and Biomedicine, pp.404-408
Conference details: Association for Computer Machinery (ACM) International Conference on Bioinformatics, Computational Biology and Biomedicine (BCB' 11), 2011 (Chicago, United States, 31-Jul-2011–03-Aug-2011)
Publisher: Association for Computer Machinery
Date published: 2011
DOI: 10.1145/2147805.2147859
ISBN: 9781450307963
Organisation Unit: School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; School of Science, Technology and Engineering; Centre for Bioinnovation
Language: English
Record Identifier: 99450150202621
Output Type: Conference paper

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