Accelerated probabilistic inference of RNA structure evolution

BMC Bioinformatics

Table 1 A stochastic context-free grammar for generating pairwise alignments of RNA structures.

L	→	R	(L → R)
Stem	→		stemExtend (1 - stemGap) basepairSubstitution [AC, BD]
	\|		stemExtend (stemGap/2) basepairIndel [AC]
	\|		stemExtend (stemGap/2) basepairIndel [BD]
	\|		(1 - stemExtend)(1 - bifurcate) baseSubstitution [AB]
	\|	Stem Stem	(1 - stemExtend) bifurcate
Loop	→		loopExtend (1 - loopGap) baseSubstitution [AB]
	\|		loopExtend (loopGap/2) baseIndel [A]
	\|		loopExtend (loopGap/2) baseIndel [B]
	\|	ε	1 - loopExtend

ISSN: 1471-2105