@Article{Bompfuenewerer:_variat_rna_foldin_align:JMathB07,
  author =	 {Athanasius F. Bompf{\"u}newerer and Rolf Backofen and Stephan H. Bernhart and 
                  Jana Hertel and Ivo L. Hofacker and Peter F. Stadler and Sebastian Will},
  title =	 {Variations on {RNA} folding and alignment: lessons from 
                  {Benasque}},
  journal =	 {Journal of Mathematical Biology},
  issn =         {0303-6812},
  year =	 2008,
  volume =	 56,
  number =	 {1-2},
  pages =	 {129-144},
  user =	 {backofen},
  pmid =	 17611759,
  doi = 	 {10.1007/s00285-007-0107-5},
  abstract =	 {Dynamic programming algorithms solve many standard problems 
                  of RNA bioinformatics in polynomial time. In this 
                  contribution we discuss a series of variations on these 
                  standard methods that implement refined biophysical models, 
                  such as a restriction of RNA folding to canonical 
                  structures, and an extension of structural alignments to an 
                  explicit scoring of stacking propensities. Furthermore, we 
                  demonstrate that a local structural alignment can be 
                  employed for ncRNA gene finding. In this context we discuss 
                  scanning variants for folding and alignment algorithms.}
}