RNA structure prediction and structural motifs analysis are challenging tasks in the investigation of RNA
We propose a novel procedure to detect structural motifs shared between two RNAs (a reference and a target). In
particular, we developed two core modules: (i) nbRSSP_extractor, to assign a unique structure to the reference RNA
encoded by a set of non-branching structures; (ii) SSD_finder, to detect structural motifs that the target RNA shares with
the reference, by means of a new score function that rewards the relative distance of the target non-branching structures
compared to the reference ones. We integrated these algorithms with already existing software to reach a coherent pipeline
able to perform the following two main tasks: prediction of RNA structures (integration of RNALfold and
nbRSSP_extractor) and search for chains of matches (integration of Structator and SSD_finder).
Keywords: Common structural motifs, dynamic programming, long non-coding RNA, RNA local structure prediction, RNA
structure comparison, RNA secondary structure.
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