Partition function for RNA secondary structure

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• Base pairs (i,j) with high Boltzmann pair probabilities are more likely to be in the phylogenetic structure (comparative sequence analysis) – observation of D. Mathews in RNA 10:1178-1190 (2004) • Similar to observation of Vingron and Argos that positions i,j in optimal pairwise sequence alignment with high Boltzmann probability are biologically relevant positions. Peter Clote July 2007
Higher probability base pairs are more likely to be in phylogenetic structure Mathews, Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization, RNA 10:1178-1190 (2004) Peter Clote July 2007
Page 1 and 2: Partition function for RNA secondar
Page 3 and 4: McCaskill’s Algorithm Peter Clote
Page 5 and 6: Peter Clote July 2007
Page 11 and 12: McCaskill’s algorithm base pairin
Page 23 and 24: Dirks, Pierce, “A partition funct
Page 29: Applications of Boltzmann partition
Page 33 and 34: Mathews, Using an RNA secondary str
Page 35 and 36: • Pr[j is unpaired] Z i,j-1 /Z i,
Page 39 and 40: Applications of sampling (Ding-Lawr
Page 41 and 42: Sample output from Sfold Peter Clot
Page 43 and 44: Sampled base pair histogram from 10
Page 45 and 46: Hairpin frequency in Ala-tRNA sampl
Page 47 and 48: Boltzmann centroids Ding, Chan, Law
Page 49 and 50: Ding, Chan, Lawrence, RNA secondary
Page 51 and 52: Ding, Chan, Lawrence, RNA secondary
Page 53: Ding, Chan, Lawrence, RNA secondary

Partition function for RNA secondary structure

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