CopomuS—Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments
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 co...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-05-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/11/3852 |
| _version_ | 1797566729476374528 |
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| author | Martin Raden Fabio Gutmann Michael Uhl Rolf Backofen |
| author_facet | Martin Raden Fabio Gutmann Michael Uhl Rolf Backofen |
| author_sort | Martin Raden |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T19:31:30Z |
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| id | doaj.art-57509333f84942a2aa3453fcb4c7d833 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T19:31:30Z |
| publishDate | 2020-05-01 |
| publisher | MDPI AG |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-57509333f84942a2aa3453fcb4c7d8332023-11-20T02:05:36ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-05-012111385210.3390/ijms21113852CopomuS—Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification ExperimentsMartin Raden0Fabio Gutmann1Michael Uhl2Rolf Backofen3Bioinformatics, Department of Computer Science, University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, GermanyBioinformatics, Department of Computer Science, University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, GermanyBioinformatics, Department of Computer Science, University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, GermanyBioinformatics, Department of Computer Science, University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, GermanyIn 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.https://www.mdpi.com/1422-0067/21/11/3852RNA-RNA interactioncompensatory mutationmutationdesignsRNA |
| spellingShingle | Martin Raden Fabio Gutmann Michael Uhl Rolf Backofen CopomuS—Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments International Journal of Molecular Sciences RNA-RNA interaction compensatory mutation mutation design sRNA |
| title | CopomuS—Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments |
| title_full | CopomuS—Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments |
| title_fullStr | CopomuS—Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments |
| title_full_unstemmed | CopomuS—Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments |
| title_short | CopomuS—Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments |
| title_sort | copomus ranking compensatory mutations to guide rna rna interaction verification experiments |
| topic | RNA-RNA interaction compensatory mutation mutation design sRNA |
| url | https://www.mdpi.com/1422-0067/21/11/3852 |
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