title: RNASAlign: RNA structural alignment system.
abstract: BACKGROUND
  Structural alignment of RNA is found to be a useful computational technique for idenitfying non-coding RNAs (ncRNAs). However, existing tools do not handle structures with pseudoknots. Although algorithms exist that can handle structural alignment for different types of pseudoknots, no software tools are available and users have to determine the type of pseudoknots to select the appropriate algoirthm to use which limits the usage of structural alignment in identifying novel ncRNAs.
  
  
  RESULTS
  We implemented the first web server, RNASAlign, which can automatically identify the pseudoknot type of a secondary structure and perform structural alignment of a folded RNA with every region of a target DNA/RNA sequence. Regions with high similarity scores and low e-values, together with the detailed alignments will be reported to the user. Experiments on more than 350 ncRNA families show that RNASAlign is effective.
  
  
  BACKGROUND
  http://www.bio8.cs.hku.hk/RNASAlign.
authors.affiliation: Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong.
authors.forename: Thomas K F
authors.initials: TK
authors.lastname: Wong
authors.forename: Kwok-Lung
authors.initials: KL
authors.lastname: Wan
authors.forename: Bay-Yuan
authors.initials: BY
authors.lastname: Hsu
authors.forename: Brenda W Y
authors.initials: BW
authors.lastname: Cheung
authors.forename: Wing-Kai
authors.initials: WK
authors.lastname: Hon
authors.forename: Tak-Wah
authors.initials: TW
authors.lastname: Lam
authors.forename: Siu-Ming
authors.initials: SM
authors.lastname: Yiu
mesh_terms: D000465:Algorithms; D020407:Internet; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D022661:RNA, Untranslated