Sept. 16, 2015, 3 a.m. by Rosalind Team
Topics: HMM
Given: A threshold θ and a pseudocount σ, 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, σ).
0.358 0.01 -------- A B C D E -------- ADA ADA AAA ADC -DA D-A
S I0 M1 D1 I1 M2 D2 I2 M3 D3 I3 E
S 0 0.01 0.819 0.172 0 0 0 0 0 0 0 0
I0 0 0.333 0.333 0.333 0 0 0 0 0 0 0 0
M1 0 0 0 0 0.01 0.786 0.204 0 0 0 0 0
D1 0 0 0 0 0.01 0.981 0.01 0 0 0 0 0
I1 0 0 0 0 0.333 0.333 0.333 0 0 0 0 0
M2 0 0 0 0 0 0 0 0.01 0.981 0.01 0 0
D2 0 0 0 0 0 0 0 0.01 0.981 0.01 0 0
I2 0 0 0 0 0 0 0 0.333 0.333 0.333 0 0
M3 0 0 0 0 0 0 0 0 0 0 0.01 0.99
D3 0 0 0 0 0 0 0 0 0 0 0.5 0.5
I3 0 0 0 0 0 0 0 0 0 0 0.5 0.5
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 0.2 0.2 0.2 0.2 0.2
M1 0.771 0.01 0.01 0.2 0.01
D1 0 0 0 0 0
I1 0.2 0.2 0.2 0.2 0.2
M2 0.2 0.01 0.01 0.771 0.01
D2 0 0 0 0 0
I2 0.2 0.2 0.2 0.2 0.2
M3 0.803 0.01 0.168 0.01 0.01
D3 0 0 0 0 0
I3 0.2 0.2 0.2 0.2 0.2
E 0 0 0 0 0