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IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions

The IntaRNA algorithm enables fast and accurate prediction of RNA–RNA hybrids by incorporating seed constraints and interaction site accessibility. Here, we introduce IntaRNAv2, which enables enhanced parameterization as well as fully customizable control over the prediction modes and output formats...

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Detalles Bibliográficos
Autores principales: Mann, Martin, Wright, Patrick R., Backofen, Rolf
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570192/
https://www.ncbi.nlm.nih.gov/pubmed/28472523
http://dx.doi.org/10.1093/nar/gkx279
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author Mann, Martin
Wright, Patrick R.
Backofen, Rolf
author_facet Mann, Martin
Wright, Patrick R.
Backofen, Rolf
author_sort Mann, Martin
collection PubMed
description The IntaRNA algorithm enables fast and accurate prediction of RNA–RNA hybrids by incorporating seed constraints and interaction site accessibility. Here, we introduce IntaRNAv2, which enables enhanced parameterization as well as fully customizable control over the prediction modes and output formats. Based on up to date benchmark data, the enhanced predictive quality is shown and further improvements due to more restrictive seed constraints are highlighted. The extended web interface provides visualizations of the new minimal energy profiles for RNA–RNA interactions. These allow a detailed investigation of interaction alternatives and can reveal potential interaction site multiplicity. IntaRNAv2 is freely available (source and binary), and distributed via the conda package manager. Furthermore, it has been included into the Galaxy workflow framework and its already established web interface enables ad hoc usage.
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spelling pubmed-55701922017-08-29 IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions Mann, Martin Wright, Patrick R. Backofen, Rolf Nucleic Acids Res Web Server Issue The IntaRNA algorithm enables fast and accurate prediction of RNA–RNA hybrids by incorporating seed constraints and interaction site accessibility. Here, we introduce IntaRNAv2, which enables enhanced parameterization as well as fully customizable control over the prediction modes and output formats. Based on up to date benchmark data, the enhanced predictive quality is shown and further improvements due to more restrictive seed constraints are highlighted. The extended web interface provides visualizations of the new minimal energy profiles for RNA–RNA interactions. These allow a detailed investigation of interaction alternatives and can reveal potential interaction site multiplicity. IntaRNAv2 is freely available (source and binary), and distributed via the conda package manager. Furthermore, it has been included into the Galaxy workflow framework and its already established web interface enables ad hoc usage. Oxford University Press 2017-07-03 2017-05-04 /pmc/articles/PMC5570192/ /pubmed/28472523 http://dx.doi.org/10.1093/nar/gkx279 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Web Server Issue
Mann, Martin
Wright, Patrick R.
Backofen, Rolf
IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions
title IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions
title_full IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions
title_fullStr IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions
title_full_unstemmed IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions
title_short IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions
title_sort intarna 2.0: enhanced and customizable prediction of rna–rna interactions
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570192/
https://www.ncbi.nlm.nih.gov/pubmed/28472523
http://dx.doi.org/10.1093/nar/gkx279
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