@article{Mann_Wright_Backofen-IntaR_enhan_and-NAR2017,
author = {Mann, Martin and Wright, Patrick R. and Backofen, Rolf},
title = {{IntaRNA} 2.0: enhanced and customizable prediction of 
         {RNA}-{RNA} interactions},
journal = {NAR},
year = {2017},
doi = {10.1093/nar/gkx279},
volume = {45},
user = {wrightp},
pmid = {28472523},
pages = {W435-W439},
number = {W1},
issn = {1362-4962},
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.}
}