A computational approach to finding RNA tertiary motifs in genomic sequences: A case study

Kevin Byron, Christian Laing, Dongrong Wen, Jason T.L. Wang

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Motif finding in DNA, RNA and proteins plays an important role in life science research. Recent patents concerning motif finding in biomolecular data are recorded in the DNA Patent Database which serves as a resource for policy makers and members of the general public interested in fields like genomics, genetics and biotechnology. In this paper, we present a computational approach to mining for RNA tertiary motifs in genomic sequences. Specifically, we describe a method, named CSminer, and show, as a case study, the application of CSminer to genome-wide search for coaxial helical stackings in RNA 3-way junctions. A coaxial helical stacking occurs in an RNA 3-way junction where two separate helical elements form a pseudocontiguous helix and provide thermodynamic stability to the RNA molecule as a whole. Experimental results demonstrate the effectiveness of our approach.

Original languageEnglish (US)
Pages (from-to)115-122
Number of pages8
JournalRecent Patents on DNA and Gene Sequences
Volume7
Issue number2
DOIs
StatePublished - Aug 28 2013

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Molecular Biology
  • Genetics(clinical)

Keywords

  • Coaxial helical stacking
  • Genome-wide motif finding
  • RNA junction

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