title: A computational approach to finding RNA tertiary motifs in genomic sequences: a case study.
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.
authors.affiliation: Bioinformatics Program and Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Byron
authors.forename: Christian
authors.initials: C
authors.lastname: Laing
authors.forename: Dongrong
authors.initials: D
authors.lastname: Wen
authors.forename: Jason T L
authors.initials: JT
authors.lastname: Wang
mesh_terms: D001483:Base Sequence; D019847:Chromosomes, Archaeal / Q000235:genetics; D019295:Computational Biology; D019613:Haloarcula / Q000235:genetics; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D010330:Patents as Topic; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA