A new family of metrics for biopolymer contact structures

Authors:
M. LlabréS;F. Rosselló
Affiliations:
Department of Mathematics and Computer Science, Research Institute of Health Science (IUNICS), University of the Balearic Islands, Palma de Mallorca E-07071, Spain;Department of Mathematics and Computer Science, Research Institute of Health Science (IUNICS), University of the Balearic Islands, Palma de Mallorca E-07071, Spain
Venue:
Computational Biology and Chemistry
Year:
2004

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A family of metrics for biopolymers based on counting independent sets

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Reidys' and Stadler's metricsfor RNA contact structures

Mathematical and Computer Modelling: An International Journal

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Abstract

Contact structures are simplified representations of biopolymers' three-dimensional structures. In this paper we introduce a new family of metrics (d"m)"m"="3 for contact structures of a fixed length, based on their representation by means of edge ideals of a polynomial ring, that generalize Reidys and Stadler's subgroup metric for RNA secondary structures. We study some abstract properties of these metrics, and we obtain explicit descriptions of them for some values of m.