A method for discovering common patterns from two RNA secondary structures and its application to structural repeat detection

Document Type

Article

Publication Date

8-1-2012

Abstract

We propose an ab initio method, named DiscoverR, for finding common patterns from two RNA secondary structures. The method works by representing RNA secondary structures as ordered labeled trees and performs tree pattern discovery using an efficient dynamic programming algorithm. DiscoverR is able to identify and extract the largest common substructures from two RNA molecules having different sizes without prior knowledge of the locations and topologies of these substructures. We also extend DiscoverR to find repeated regions in an RNA secondary structure, and apply this extended method to detect structural repeats in the 3′-untranslated region of a protein kinase gene. We describe the biological significance of a repeated hairpin found by our method, demonstrating the usefulness of the method. DiscoverR is implemented in Java; a jar file including the source code of the program is available for download at http://bioinformatics.njit.edu/DiscoverR. © 2012 Imperial College Press.

Identifier

84863989902 (Scopus)

Publication Title

Journal of Bioinformatics and Computational Biology

External Full Text Location

https://doi.org/10.1142/S0219720012500011

e-ISSN

17576334

ISSN

02197200

PubMed ID

22809414

Issue

4

Volume

10

Grant

ZIABC008382

Fund Ref

National Institutes of Health

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