Current Bioinformatics

Yi-Ping Phoebe Chen
Department of Computer Science and Information Technology
La Trobe University
Melbourne
Australia

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A New Procedure to Analyze RNA Non-Branching Structures

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

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).

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

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Article Details

VOLUME: 10
ISSUE: 3
Year: 2015
Page: [242 - 258]
Pages: 17
DOI: 10.2174/1574893609666140820224651
Price: $58