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

Martin Mann; Patrick R Wright; Rolf Backofen

doi:10.1093/nar/gkx279

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

Nucleic Acids Res. 2017 Jul 3;45(W1):W435-W439. doi: 10.1093/nar/gkx279.

Authors

Martin Mann¹, Patrick R Wright¹, Rolf Backofen^{1

2}

Affiliations

¹ Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany.
² Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Genome
Internet
RNA / chemistry*
Software*

Substances

RNA