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Table 1 Table 1

From: A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure

State type

Description

Production

Emission

Transition

P

(pair emitting)

P → aYb

e v (a,b)

t v (Y)

L

(left emitting)

L → aY

e v (a)

t v (Y)

R

(right emitting)

R → Ya

e v (a)

t v (Y)

B

(bifurcation)

B → SS

1

1

D

(delete)

D → Y

1

t v (Y)

S

(start)

S → Y

1

t v (Y)

E

(end)

E → ε

1

1