Variations on RNA folding and alignment: lessons from Benasque
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- Bompfünewerer, A.F., Backofen, R., Bernhart, S.H. et al. J. Math. Biol. (2008) 56: 129. doi:10.1007/s00285-007-0107-5
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.