Sept. 16, 2015, 3 a.m. by Rosalind Team
Topics: HMM
Given: A threshold θ, followed by an alphabet Σ, followed by a multiple alignment Alignment whose strings are formed from Σ.
Return: The transition and emission probabilities of the profile HMM HMM(Alignment, θ).
0.289 -------- A B C D E -------- EBA EBD EB- EED EBD EBE E-D EBD
S I0 M1 D1 I1 M2 D2 I2 M3 D3 I3 E
S 0 0 1.0 0 0 0 0 0 0 0 0 0
I0 0 0 0 0 0 0 0 0 0 0 0 0
M1 0 0 0 0 0 0.875 0.125 0 0 0 0 0
D1 0 0 0 0 0 0 0 0 0 0 0 0
I1 0 0 0 0 0 0 0 0 0 0 0 0
M2 0 0 0 0 0 0 0 0 0.857 0.143 0 0
D2 0 0 0 0 0 0 0 0 1.0 0 0 0
I2 0 0 0 0 0 0 0 0 0 0 0 0
M3 0 0 0 0 0 0 0 0 0 0 0 1.0
D3 0 0 0 0 0 0 0 0 0 0 0 1.0
I3 0 0 0 0 0 0 0 0 0 0 0 0
E 0 0 0 0 0 0 0 0 0 0 0 0
--------
A B C D E
S 0 0 0 0 0
I0 0 0 0 0 0
M1 0 0 0 0 1.0
D1 0 0 0 0 0
I1 0 0 0 0 0
M2 0 0.857 0 0 0.143
D2 0 0 0 0 0
I2 0 0 0 0 0
M3 0.143 0 0 0.714 0.143
D3 0 0 0 0 0
I3 0 0 0 0 0
E 0 0 0 0 0