Accelerated probabilistic inference of RNA structure evolution

Holmes, Ian

doi:10.1186/1471-2105-6-73

BMC Bioinformatics

Table 2 The stemloc grammar, part 1 of 3: stem and loop structures.

From: Accelerated probabilistic inference of RNA structure evolution

L	→	R	(L → R)
Start	→	Stem	startInStem
	\|	LBulge	(1 - startInStem) postStem [2]/ (2 postStem[i])
	\|	RBulge	(1 - startInStem) postStem[2]/ (2 postStem[i])
	\|	LRBulge	(1 - startInStem) postStem [3]/ ( postStem[i])
	\|	Multi	(1 - startInStem) postStem [4]/ ( postStem[i])
Stem	→	^xyStemMatch	1 - stemGapOpen
	\|	^yStemIns	stemGapOpen/2
	\|	^xStemDel	stemGapOpen/2
StemMatch	→	^xyStemMatch	(1 - stemGapOpen) stemExtend
	\|	^yStemIns	stemGapOpen/2
	\|	^xStemDel	stemGapOpen/2
	\|	StemExit	(1 - stemGapOpen)(1 - stemExtend)
StemIns	→	^xyStemMatch	(1 - stemGapExtend)(1 - stemGapSwap) stemExtend
	\|	^yStemIns	stemGapExtend
	\|	^xStemDel	(1 - stemGapExtend) stemGapSwap
	\|	StemExit	(1 - stemGapExtend) (1 - stemGapSwap)(1 - stemExtend)
StemDel	→	^xyStemMatch	(1 - stemGapExtend)(1 - stemGapSwap) stemExtend
	\|	^xStemDel	stemGapExtend
	\|	^yStemIns	(1 - stemGapExtend) stemGapSwap
	\|	StemExit	(1 - stemGapExtend) stemGapSwap (1 - stemExtend)
StemExit	→	Loop	postStem [1]
	\|	LBulge	postStem [2]/2
	\|	RBulge	postStem [2]/2
	\|	LRBulge	postStem [3]
	\|	Multi	postStem [4]
Multi	→	LMulti RMulti	1
LMulti	→	LBulge	multiBulgeOpen
	\|	Stem	(1 - multiBulgeOpen)
RMulti	→	Multi	multiExtend
	\|	Stem	(1 - multiExtend)(1 - multiBulgeOpen)²
	\|	LBulge	(1 - multiExtend)(1 - multiBulgeOpen) multiBulgeOpen
	\|	RBulge	(1 - multiExtend)(1 - multiBulgeOpen) multiBulgeOpen
	\|	LRBulge	(1 - multiExtend) multiBulgeOpen²
Loop	→	^xyLoopMatch	(1 - loopGapOpen)
	\|	^yLoopIns	loopGapOpen/2
	\|	^xLoopDel	loopGapOpen/2
LoopMatch	→	^xyLoopMatch	(1 - loopGapOpen) loopExtend
	\|	^yLoopIns	loopGapOpen/2
	\|	^xLoopDel	loopGapOpen/2
	\|	ε	(1 - loopGapOpen) (1 - loopExtend)
LoopIns	→	^xyLoopMatch	(1 - loopGapExtend)(1 - loopGapSwap) loopExtend
	\|	^yLoopIns	loopGapExtend
	\|	^xLoopDel	(1 - loopGapExtend) loopGapSwap
	\|	ε	(1 - loopGapExtend)(1 - loopGapSwap) (1 - loopExtend)
LoopDel	→	^xyLoopMatch	(1 - loopGapExtend)(1 - loopGapSwap) loopExtend
	\|	^xLoopDel	loopGapExtend
	\|	^yLoopIns	(1 - loopGapExtend) loopGapSwap
	\|	ε	(1 - loopGapExtend)(1 - loopGapSwap)(1 - loopExtend)

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ISSN: 1471-2105

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