@article{4070,
  title = {SCARNA: Fast and Accurate Structural Alignment of RNA Sequences by Matching Fixed-Length Stem Fragments},
  journal = {Bioinformatics},
  abstract = {The functions of non-coding RNAs
  are strongly related to their secondary structures,
  but it is known
  that a secondary structure prediction of a single sequence is not reliable.
  Therefore, we have to collect similar RNA sequences
  with a common secondary structure
  for the analyses of a new non-coding RNA
  without knowing the exact secondary structure itself.
  Therefore, the sequence comparison in searching similar RNAs should consider
  not only their sequence similarities but their potential secondary structures.
  Sankoff‘s algorithm predicts the common secondary structures of the sequences,
  but it is computationally too expensive to apply to large-scale analyses.
  Because we often want to compare a large number of cDNA sequences
  or to search similar RNAs in the whole genome sequences,
  much faster algorithms are required.
  We propose a new method of comparing RNA sequences
  based on the structural alignments
  of the fixed-length fragments of the stem candidates.
  The implemented software,
  SCARNA (Stem Candidate Aligner for RNAs),
  is fast enough to apply to the long sequences
  in the large-scale analyses.
  The accuracy of the alignments is better or comparable
  to the much slower existing algorithms.},
  volume = {22},
  number = {14},
  pages = {1723-1729},
  organization = {Max-Planck-Gesellschaft},
  school = {Biologische Kybernetik},
  month = may,
  year = {2006},
  slug = {4070},
  author = {Tabei, Y. and Tsuda, K. and Kin, T. and Asai, K.},
  month_numeric = {5}
}