CopomuS-Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments.
Int J Mol Sci
; 21(11)2020 May 28.
Article
en En
| MEDLINE
| ID: mdl-32481751
ABSTRACT
In silico RNA-RNA interaction prediction is widely applied to identify putative interaction partners and to assess interaction details in base pair resolution. To verify specific interactions, in vitro evidence can be obtained via compensatory mutation experiments. Unfortunately, the selection of compensatory mutations is non-trivial and typically based on subjective ad hoc decisions. To support the decision process, we introduce our COmPensatOry MUtation Selector CopomuS. CopomuS evaluates the effects of mutations on RNA-RNA interaction formation using a set of objective criteria, and outputs a reliable ranking of compensatory mutation candidates. For RNA-RNA interaction assessment, the state-of-the-art IntaRNA prediction tool is applied. We investigate characteristics of successfully verified RNA-RNA interactions from the literature, which guided the design of CopomuS. Finally, we evaluate its performance based on experimentally validated compensatory mutations of prokaryotic sRNAs and their target mRNAs. CopomuS predictions highly agree with known results, making it a valuable tool to support the design of verification experiments for RNA-RNA interactions. It is part of the IntaRNA package and available as stand-alone webserver for ad hoc application.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Programas Informáticos
/
ARN
/
ARN Bacteriano
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Biología Computacional
/
Mutación
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
Int J Mol Sci
Año:
2020
Tipo del documento:
Article
País de afiliación:
Alemania