- The profile HMM is:
-
- /\ /\ /\ /\ /\
- I[0] I[1] I[k-1] I[k] I[L]
- ^ \ ^ \ \ ^ \ ^ \ \ ^
- | \ | \ \ | \ | \ \ |
- M[0] -> M[1] -> ... -> M[k-1] -> M[k] -> ... -> M[L] M[L+1]
- \ \/ \/ \/ \/ /
- \ /\ /\ /\ /\ /
- D[1] -> -> D[k-1] -> D[k] ->
- \/ \/ \/
-
- Every {M,I}[k], k=0..L connects M[L+1] at the same probability, while
- no D[k], k=1..L-1 connects M[L+1]. This means an alignment can end up
- with M or I but not D.
-
- Deletions are dumb states which do not emit residues. Frankly, I am
- not sure if they are handled properly in the following
- implementation. This is a potential concern to be resolved in future.
+ The topology of the profile HMM:
+
+ /\ /\ /\ /\
+ I[1] I[k-1] I[k] I[L]
+ ^ \ \ ^ \ ^ \ \ ^
+ | \ \ | \ | \ \ |
+ M[0] M[1] -> ... -> M[k-1] -> M[k] -> ... -> M[L] M[L+1]
+ \ \/ \/ \/ /
+ \ /\ /\ /\ /
+ -> D[k-1] -> D[k] ->
+ \/ \/
+
+ M[0] points to every {M,I}[k] and every {M,I}[k] points M[L+1].