/
pfold-loopmodel.eg
45 lines (41 loc) · 1.41 KB
/
pfold-loopmodel.eg
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(alphabet
(name RNA)
(token (a c g u))
(complement (u g c a))
(extend (to n) (from a) (from c) (from g) (from u))
(extend (to x) (from a) (from c) (from g) (from u))
(extend (to t) (from u))
(extend (to r) (from a) (from g))
(extend (to y) (from c) (from u))
(extend (to m) (from a) (from c))
(extend (to k) (from g) (from u))
(extend (to s) (from c) (from g))
(extend (to w) (from a) (from u))
(extend (to h) (from a) (from c) (from u))
(extend (to b) (from c) (from g) (from u))
(extend (to v) (from a) (from c) (from g))
(extend (to d) (from a) (from g) (from u))
(wildcard *)
) ;; end alphabet RNA
(chain
(update-policy rev)
(terminal (NUC))
;; initial probability distribution
(initial (state (a)) (prob 0.364097))
(initial (state (c)) (prob 0.151009))
(initial (state (g)) (prob 0.211881))
(initial (state (u)) (prob 0.273013))
;; mutation rates
(mutate (from (a)) (to (c)) (rate 0.099))
(mutate (from (a)) (to (g)) (rate 0.322))
(mutate (from (a)) (to (u)) (rate 0.263))
(mutate (from (c)) (to (a)) (rate 0.239))
(mutate (from (c)) (to (g)) (rate 0.242))
(mutate (from (c)) (to (u)) (rate 0.927))
(mutate (from (g)) (to (a)) (rate 0.553))
(mutate (from (g)) (to (c)) (rate 0.173))
(mutate (from (g)) (to (u)) (rate 0.396))
(mutate (from (u)) (to (a)) (rate 0.351))
(mutate (from (u)) (to (c)) (rate 0.513))
(mutate (from (u)) (to (g)) (rate 0.307))
) ;; end chain NUC