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Christian Reidys, Nankai University Wednesday November 12, 2008 3:05pm in LCB 215 "Canonical pseudoknot RNA structure: Combinatorics and folding" Abstract: We introduce a biophysically relevant class of RNA pseudoknot structures by requiring a minimal number of arcs contained in a stack. We present the exact and asymptotical enumeration of these canonical RNA structures, analyze their basic statistics and then discuss how minimum-free energy structures can be found. In the process we discuss a novel folding algorithm, cross, which folds 3-noncrossing, 3-canonical RNA structures over 100 nucleotides in an average time of 2:30 min. |