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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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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. |
format | Online Article Text |
id | pubmed-5570192 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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