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