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Resolution: standard / high Figure 2.
Example parse trees for four different unambiguous grammars, G3-G6. Each grammar's production rules defines how the example structure will be described.
Some aspects seem artificial, having more to do with the constraints of being unambiguous
rather than biologically meaningful features of RNA. G3 must bifurcate to accomodate
a bulge on one side, but not the other. G4 shows a stutter-step behavior in stems,
with a cycle of S ⇒ T ⇒ aS
productions for each base pair. G5 (rightmost) uses a bifurcation and a null production
for every base pair. G6 uses bifurcations at every single stranded residue.
Dowell and Eddy BMC Bioinformatics 2004 5:71 doi:10.1186/1471-2105-5-71 |