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dc.contributor.authorMartin, Nora S
dc.contributor.authorAhnert, Sebastian
dc.date.accessioned2022-06-15T09:00:18Z
dc.date.available2022-06-15T09:00:18Z
dc.date.issued2022-06
dc.date.submitted2022-01-24
dc.identifier.issn1742-5689
dc.identifier.otherrsif20220072
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/338109
dc.descriptionFunder: Winton Programme for the Physics of Sustainability
dc.descriptionFunder: Gates Cambridge Trust; Id: http://dx.doi.org/10.13039/501100005370
dc.description.abstractThe genotype-phenotype (GP) map of RNA secondary structure links each RNA sequence to its corresponding secondary structure. Previous research has shown that the large-scale structural properties of GP maps, such as the size of neutral sets in genotype space, can influence evolutionary outcomes. In order to use neutral set sizes, efficient and accurate computational methods are needed to compute them. Here, we propose a new method, which is based on free energy estimates and is much faster than existing sample-based methods. Moreover, this approach can give insight into the reasons behind neutral set size variations, for example, why structures with fewer stacks tend to have larger neutral set sizes. In addition, we generalize neutral set size calculations from the previously studied many-to-one framework, where each sequence folds into a single energetically preferred structure, to a fuller many-to-many framework, where several low-energy structures are included. We find that structures with high neutral sets in one framework also tend to have large neutral sets in the other framework for a range of parameters and thus the choice of GP map does not fundamentally affect which structures have the largest neutral set sizes.
dc.languageen
dc.publisherThe Royal Society
dc.subjectLife Sciences–Physics interface
dc.subjectResearch articles
dc.subjectRNA secondary structure
dc.subjectsequence–structure map
dc.subjectgenotype–phenotype map
dc.subjectneutral set
dc.titleFast free-energy-based neutral set size estimates for the RNA genotype-phenotype map.
dc.typeArticle
dc.date.updated2022-06-15T09:00:18Z
prism.issueIdentifier191
prism.publicationNameJ R Soc Interface
prism.volume19
dc.identifier.doi10.17863/CAM.85518
dcterms.dateAccepted2022-05-23
rioxxterms.versionofrecord10.1098/rsif.2022.0072
rioxxterms.versionAO
rioxxterms.versionVoR
rioxxterms.licenseref.urihttp://creativecommons.org/licenses/by/4.0/
dc.contributor.orcidMartin, Nora S [0000-0003-4026-0985]
dc.contributor.orcidAhnert, Sebastian [0000-0003-2613-0041]
dc.identifier.eissn1742-5662
pubs.funder-project-idGatsby Charitable Foundation (PTAG/021)
cam.issuedOnline2022-06-15


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