The impact of various seed accessibility and interaction constraints on sRNA target prediction- a systematic assessment

摘要

Prediction of RNA-RNA interactions is a versatile approach to detect putative targets of non-coding RNAs [ ]. Accessibility-based approaches combine the prediction of a most stable interaction duplex with an energy penalty for making the interaction regions accessible, i.e. free of intra-molecular structure. They are very good compromise between the computational complex prediction of joint structures and a simple detection of stable duplexes. While accessibility-based approaches that further incorporate seed constraints are best suited for in silico target screens of prokaryotic sRNAs [ ], available programs implement different (sets of) constraints and respective thresholds to increase the prediction accuracy. Although there are various studies that compare tools (based on their default parameters) [ – ], so far no study investigated the impact and potential of the different constraints in a systematic way. This is needed to both provide users with an intuition how the constraints influence the prediction results and to guide the development and improvement of current and future tools.