title: A method for aligning RNA secondary structures and its application to RNA motif detection.
abstract: BACKGROUND
  Alignment of RNA secondary structures is important in studying functional RNA motifs. In recent years, much progress has been made in RNA motif finding and structure alignment. However, existing tools either require a large number of prealigned structures or suffer from high time complexities. This makes it difficult for the tools to process RNAs whose prealigned structures are unavailable or process very large RNA structure databases.
  
  
  RESULTS
  We present here an efficient tool called RSmatch for aligning RNA secondary structures and for motif detection. Motivated by widely used algorithms for RNA folding, we decompose an RNA secondary structure into a set of atomic structure components that are further organized by a tree model to capture the structural particularities. RSmatch can find the optimal global or local alignment between two RNA secondary structures using two scoring matrices, one for single-stranded regions and the other for double-stranded regions. The time complexity of RSmatch is O(mn) where m is the size of the query structure and n that of the subject structure. When applied to searching a structure database, RSmatch can find similar RNA substructures, and is capable of conducting multiple structure alignment and iterative database search. Therefore it can be used to identify functional RNA motifs. The accuracy of RSmatch is tested by experiments using a number of known RNA structures, including simple stem-loops and complex structures containing junctions.
  
  
  CONCLUSIONS
  With respect to computing efficiency and accuracy, RSmatch compares favorably with other tools for RNA structure alignment and motif detection. This tool shall be useful to researchers interested in comparing RNA structures obtained from wet lab experiments or RNA folding programs, particularly when the size of the structure dataset is large.
authors.affiliation: Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ 07101, USA. jl7@oak.njit.edu
authors.forename: Jianghui
authors.initials: J
authors.lastname: Liu
authors.forename: Jason T L
authors.initials: JT
authors.lastname: Wang
authors.forename: Jun
authors.initials: J
authors.lastname: Hu
authors.forename: Bin
authors.initials: B
authors.lastname: Tian
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D017124:Conserved Sequence; D030541:Databases, Genetic; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D022661:RNA, Untranslated; D038621:Regulatory Sequences, Ribonucleic Acid; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D022661:RNA, Untranslated; D038621:Regulatory Sequences, Ribonucleic Acid; D012313:RNA