A probabilistic model for the evolution of RNA structure

BMC Bioinformatics

Table 1 Classes of degeneracy in the Structure Tree grammars. Permutations and combinations of these cycles are also possible.

Degeneracy	Figure	Nonterminal sequence	Rule sequence	Comment
Null cycle	5	L → S → L	2,3,5
	6	L₁ → ... → L₁	4,7,11	via S₁L₁
			5,32,30	via S₄L₁
		L₂ → ... → L₂	17,27,25
		L₁ → L₂ ...	6,27,25
		...L₂ → L₁	15,11,7	via S₁L₁
			16,32,30	via S₄L₁
		L₃ → S₃ → L₃	24,25,27
		L₄ → S₄ → L₄	29,30,32
Loop bifurcation	5	L → LL	2,5
	6	L₁ → L₁L₁	4,11
		L₂ → L₁L₁	15,11
		L₃ → L₃L₃	24,27
		L₄ → L₄L₄	29,32
Silent bulge	5	S → L → S	5,3,2	Cyclic permutation of L → S → L
	6	S₂ → L₁ → S₁	22,4,7
		S₁ → L₁ → S₁	11,4,7	Cyclic permutation of L₁ → S₁ → L₁
		S₃ → L₃ → S₃	27,24,25	Cyclic permutation of L₃ → S₃ → L₃
		S₄ → L₄ → S₄	32,29,30	Cyclic permutation of L₄ → S₄ → L₄

ISSN: 1471-2105