BACKGROUND Seed and accessibility constraints are core features to enable highly accurate sRNA target screens based on RNA-RNA interaction prediction. Currently, available tools provide different (sets of) constraints and default parameter sets. Thus, it is hard to impossible for users to estimate the influence of individual restrictions on the prediction results. RESULTS Here, we present a systematic assessment of the impact of established and new constraints on sRNA target prediction both on a qualitative as well as computational level. This is done exemplarily based on the performance of IntaRNA, one of the most exact sRNA target prediction tools. IntaRNA provides various ways to constrain considered seed interactions, e.g. based on seed length, its accessibility, minimal unpaired probabilities, or energy thresholds, beside analogous constraints for the overall interaction. Thus, our results reveal the impact of individual constraints and their combinations. CONCLUSIONS This provides both a guide for users what is important and recommendations for existing and upcoming sRNA target prediction approaches.We show on a large sRNA target screen benchmark data set that only by altering the parameter set, IntaRNA recovers 30% more verified interactions while becoming 5-times faster. This exemplifies the potential of seed, accessibility and interaction constraints for sRNA target prediction.

中文翻译：

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各种种子，可及性和相互作用限制对sRNA靶标预测的影响-系统评估。

背景技术种子和可访问性约束是基于RNA-RNA相互作用预测实现高精度sRNA靶标筛选的核心特征。当前，可用工具提供了不同的（一组）约束和默认参数集。因此，用户难以估计个别限制对预测结果的影响。结果在这里，我们在定性和计算水平上对已建立和新约束对sRNA目标预测的影响进行系统评估。基于IntaRNA的性能示例性地完成此操作，IntaRNA是最精确的sRNA靶标预测工具之一。IntaRNA提供了多种方法来限制考虑的种子相互作用，例如基于种子长度，其可及性，最小的未配对概率或能量阈值，除了整体互动的类似限制。因此，我们的结果揭示了单个约束及其组合的影响。结论这为用户提供了对现有和即将到来的sRNA靶标预测方法的重要指导和建议。我们在大型sRNA靶标筛选基准数据集上显示，仅通过更改参数集，IntaRNA可以将验证的相互作用恢复30％以上快5倍。这举例说明了种子，可及性和相互作用限制对于sRNA靶标预测的潜力。我们在大型sRNA目标筛选基准数据集上显示，仅通过更改参数集，IntaRNA就能将验证的相互作用多回收30％，而速度提高5倍。这举例说明了种子，可及性和相互作用限制对于sRNA靶标预测的潜力。我们在大型sRNA目标筛选基准数据集上显示，仅通过更改参数集，IntaRNA就能将验证的相互作用多回收30％，而速度提高5倍。这举例说明了种子，可及性和相互作用限制对于sRNA靶标预测的潜力。