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Neutral components show a hierarchical community structure in the genotype-phenotype map of RNA secondary structure.

Accepted version
Peer-reviewed

Type

Article

Change log

Authors

Weiß, Marcel 
Ahnert, Sebastian E 

Abstract

Genotype-phenotype (GP) maps describe the relationship between biological sequences and structural or functional outcomes. They can be represented as networks in which genotypes are the nodes, and one-point mutations between them are the edges. The genotypes that map to the same phenotype form subnetworks consisting of one or multiple disjoint connected components-so-called neutral components (NCs). For the GP map of RNA secondary structure, the NCs have been found to exhibit distinctive network features that can affect the dynamical processes taking place on them. Here, we focus on the community structure of RNA secondary structure NCs. Building on previous findings, we introduce a method to reveal the hierarchical community structure solely from the sequence constraints and composition of the genotypes that form a given NC. Thereby, we obtain modularity values similar to common community detection algorithms, which are much more complex. From this knowledge, we endorse a sampling method that allows a fast exploration of the different communities of a given NC. Furthermore, we introduce a way to estimate the community structure from genotype samples, which is useful when an exhaustive analysis of the NC is not feasible, as is the case for longer sequence lengths.

Description

Keywords

RNA secondary structure, community structure, genotype–phenotype map, network, Evolution, Molecular, Genotype, Phenotype, Protein Structure, Secondary, RNA

Journal Title

J R Soc Interface

Conference Name

Journal ISSN

1742-5689
1742-5662

Volume Title

17

Publisher

The Royal Society

Rights

All rights reserved
Sponsorship
Gatsby Charitable Foundation (GAT3395/CCD)
MW was supported by the EPSRC and the Gatsby Charitable Foundation. SEA was supported by the Gatsby Charitable Foundation and the Alan Turing Institute.