A transducer, , capable of global alignment with affine gap penalty.
See Transducer Legend for explanations of symbols in this diagram.
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- a + b + c = 1,
- d + e + f = 1,
- p + q + r = 1,
- v + w + x = 1.
Typically outgoing transitions from S are the same as those from M:
- a = d;
- b = e;
- c = f.
The D->I transition (weight p) is unnecessary for separable distributions over insertions & deletions, but may be desirable for several purposes:
- it appears in TKF91;
- without it, alignments like MDIM have zero likelihood, while those like MIDM do not;
- note that fp = dx required for strict symmetry, but this is NOT the case in TKF91;
- (speculatively) it may be required to approximate the serial composition of gotoh transducers (see Renormalized Transducer Composition).
- apparent support for this is the observation that it's required for reversible affine gaps in the Gotoh Pair HMM.
The W and X states are equivalent if the condition b/c = e/f = q/r = w/x is satisfied (as is the case in TKF91).
A fuller discussions of the symmetry constraints imposed by reversibility may be found on the Gotoh Pair HMM page.