title: Local structural alignment of RNA with affine gap model.
abstract: BACKGROUND
  Predicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps.
  
  
  RESULTS
  In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model. We provide the algorithm to solve the problem.
  
  
  CONCLUSIONS
  Based on an experiment, we show that there are ncRNA families in which considering local structural alignment with gap penalty model can identify real hits more effectively than using global alignment or local alignment without gap penalty model.
authors.affiliation: Department of Computer Science, The University of Hong Kong, Hong Kong. kfwong@cs.hku.hk.
authors.forename: Thomas
authors.initials: T
authors.lastname: King-Fung Wong
authors.forename: Brenda
authors.initials: B
authors.lastname: Wing-Yan Cheung
authors.forename: Tak-Wah
authors.initials: TW
authors.lastname: Lam
authors.forename: Siu-Ming
authors.initials: SM
authors.lastname: Yiu