Table 2

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

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

xy StemMatch

(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)


Holmes BMC Bioinformatics 2005 6:73   doi:10.1186/1471-2105-6-73

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