Neutral networks of sequence to shape maps

DOI10.1016/J.JTBI.2007.09.012MaRDI QIDQ1788477zbMATH OpenOpenAlexWikidataFDO

Authors Jing Qin, Christian M. Reidys, Emma Yu Jin

Publication date 8 October 2018

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0706.0760

zbMATH Keywords

bipartiteshapediametercomponentneutral networkcombinatory map

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Exact enumeration problems, generating functions (05A15)

Abstract: In this paper we present a novel framework for sequence to shape maps. These combinatorial maps realize exponentially many shapes, and have preimages which contain extended connected subgraphs of diameter n (neutral networks). We prove that all basic properties of RNA folding maps also hold for combinatorial maps. Our construction is as follows: suppose we are given a graph $H$ over the $1>\mathrm{...},n$ and an alphabet of nucleotides together with a symmetric relation $mathcalR$, implied by base pairing rules. Then the shape of a sequence of length n is the maximal H subgraph in which all pairs of nucleotides incident to H-edges satisfy $mathcalR$. Our main result is to prove the existence of at least $sqrt{2}^{n-1}$ shapes with extended neutral networks, i.e. shapes that have a preimage with diameter $n$ and a connected component of size at least $(frac1+sqrt52{)}^n+(frac1-sqrt52{)}^n$. Furthermore, we show that there exists a certain subset of shapes which carries a natural graph structure. In this graph any two shapes are connected by a path of shapes with respective neutral networks of distance one. We finally discuss our results and provide a comparison with RNA folding maps.

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Cites work

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Cited in

(1)

• An \textit{in silico} exploration of the neutral network in protein sequence space

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