Variations on RNA folding and alignment: lessons from Benasque
- First Online:
- 245 Downloads
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.
KeywordsRNA folding Secondary structure alignment Dynamic programming
Mathematics Subject Classification (2000)90C27 90C90 92C40
Unable to display preview. Download preview PDF.