# Construct a Profile HMM solved by 135

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

Topics: HMM

## Profile HMM Problem

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).

## Sample Dataset

0.289
--------
A   B   C   D   E
--------
EBA
EBD
EB-
EED
EBD
EBE
E-D
EBD


## Sample Output

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


## Extra Dataset

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