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. 2009 Aug 28;5(8):e1000483. doi: 10.1371/journal.pcbi.1000483

Table 3. State types of the branch transducer (conditionally-normalized Pair SCFG) of the TKF Structure Tree model.

State type absorb emit description
Inline graphic Inline graphic Start of a loop
Inline graphic Inline graphic Inline graphic Single-base insertion
Inline graphic Inline graphic Inline graphic Inline graphic Single-base substitution
Inline graphic Inline graphic Inline graphic Single-base deletion
Inline graphic Inline graphic Wait for next base
Inline graphic Inline graphic Start of a stem
Inline graphic Inline graphic Inline graphic Base-pair insertion
Inline graphic Inline graphic Inline graphic Inline graphic Base-pair substitution
Inline graphic Inline graphic Inline graphic Base-pair deletion
Inline graphic Inline graphic Wait for next base-pair
Inline graphic Inline graphic Inline graphic Stem insertion
Inline graphic Inline graphic Inline graphic Inline graphic Stem conservation
Inline graphic Inline graphic Inline graphic Inline graphic Stem deletion
Inline graphic Inline graphic Inline graphic Inline graphic Stem extinction

States which have the same names as states of the singlet transducer in Table 1 are the branch-transducer equivalents of the corresponding singlet-transducer states (e.g., a Inline graphic state might be the branch equivalent of an Inline graphic state). States Inline graphic and Inline graphic are the Inline graphic states of a sub-model (not shown) identical in structure to the singlet transducer. They are used to insert a new stem-loop structure.