Jukes-Cantor Model Courtesy of M. yaffe Assume each nucleotide equally likely to change into any other nt with rate of change=al Overall rate of substitution 3a A C so if g at t=0. at t=1. P=1-30 and PG(2=(1-3a PG() +a[1-PG Expanding this gives PG(=1/4+(3/4)e-4at Can show that this gives K=-3/4 In[ 1-(4/3)(p) K= true number of substitutions that have occurred P= fraction of nt that differ by a simple count Captures general behaviour
Jukes-Cantor Model Courtesy of M. Yaffe Assume each nucleotide equally likely to change into any other nt, α α with rate of change= α. Overall rate of substitution = 3α …so if G at t=0, at t=1, PG(1)=1-3α and PG(2)=(1-3α) PG(1) +α [1− PG(1) ] G T A C α α α α Expanding this gives PG(t)=1/4 + (3/4)e-4 αt Can show that this gives K = -3/4 ln[1-(4/3)(p)] K = true number of substitutions that have occurred, P = fraction of nt that differ by a simple count. Captures general behaviour…
Predicting RNA Secondary Structure Review of rna structure Motivation: ribosome gallery, miRNAS/SIRNAS Predicting 2 structure by energy minimization Predicting 2 structure by covariation Finding non-coding rna genes Read Mount. Ch, 5
Predicting RNA Secondary Structure o structure by energy minimization o structure by covariation Read Mount, Ch. 5 • Review of RNA structure - Motivation: ribosome gallery, miRNAs/siRNAs • Predicting 2 • Predicting 2 • Finding non-coding RNA genes