IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions
IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions
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DOI：
10.1093/nar/gkx279
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发表时间：
2017-07-03
影响因子：
14.9
通讯作者：
Backofen, Rolf
中科院分区：
文献类型：
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作者：
Mann, Martin;Wright, Patrick R.;Backofen, Rolf
INTARNA算法通过结合种子约束和相互作用位点的可及性，实现了对RNA-RNA杂交体的快速和准确预测。在这里，我们介绍INTARNAv2，它支持增强的参数化以及对预测模式和输出格式的完全可定制的控制。基于最新的基准数据，显示了增强的预测质量，并强调了由于更具限制性的种子限制而带来的进一步改进。扩展的网络界面为RNA-RNA相互作用提供了新的最低能量分布的可视化。这些可以对交互作用备选方案进行详细的调查，并可以揭示潜在的交互作用位置的多样性。INTARNAv2是免费提供的(源代码和二进制)，并通过CONDA包管理器分发。此外，它已被纳入银河工作流程框架，其已经建立的网络界面允许临时使用。
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.