Construct a Profile HMM with Pseudocounts solved by 76

Sept. 16, 2015, 3 a.m. by Rosalind Team

Topics: HMM

Profile HMM with Pseudocounts Problem

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).

Sample Dataset

0.358   0.01
--------
A   B   C   D   E
--------
ADA
ADA
AAA
ADC
-DA
D-A

Sample Output

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

Extra Dataset

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