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

Lei Hua, Jason T.L. Wang, Xiang Ji, Ankur Malhotra, Mugdha Khaladkar, Bruce A. Shapiro, Kaizhong Zhang

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

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.

Original languageEnglish (US)
Article number1250001
JournalJournal of Bioinformatics and Computational Biology
Volume10
Issue number4
DOIs
StatePublished - Aug 2012

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

Keywords

  • RNA secondary structure
  • pattern discovery
  • repeat finding

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