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


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

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