A New Procedure to Analyze RNA Non-Branching Structures

Title:A New Procedure to Analyze RNA Non-Branching Structures

Volume: 10 Issue: 3

Author(s): Giulia Fiscon, Paola Paci, Teresa Colombo and Giulio Iannello

Affiliation:

Keywords: Common structural motifs, dynamic programming, long non-coding RNA, RNA local structure prediction, RNA structure comparison, RNA secondary structure.

Abstract: RNA structure prediction and structural motifs analysis are challenging tasks in the investigation of RNA function.

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).

Cite this article as:

Fiscon Giulia, Paci Paola, Colombo Teresa and Iannello Giulio, A New Procedure to Analyze RNA Non-Branching Structures, Current Bioinformatics 2015; 10 (3) . https://dx.doi.org/10.2174/1574893609666140820224651