Derive parameters of profile HMM for MSA given in figure 1 I.Emission counts for

Question

Derive parameters of profile HMM for MSA given in figure 1

I.Emission counts for match states                                      

II.Emission counts for insert states                                      

III.Counts of transitions between states                                             

IV. Emission probabilities for match, insert, and hidden states         

Figure 1. Multiple sequence alignment of five DNA sequences

T--CT-

-AA-TA

T--CTA

TC-G-A

C-CGAC

Feel free to use Durbin’s Figure 5.7c format (below)

(a) Multiple alignment: (c) Observed emission/transition counts bat A G rat cat AG- AA - gnat goat A G model position 0 23 A A G- C A A A OC match emissionsG 0 0 4 nsert (b) Profile-HMM architecture: emissionsG M-M 4 3 2 4 M-D 00 M-I 0 00 I-M 0020 state transitions D 000 1-1 D-M D-D D-l 0 0 40 end Figure 5.7 As an example of model construction from an alignment, a small DNA multiple alignment is given (a), with three columns marked above with x's. These three columns are assigned to positions 1-3 in the model ar- chitecture (b). The assignment of columns to model positions determines the symbol emission and state transition counts (c) from which probability parameters would be estimated

Explanation / Answer

Answer : as per the multiple sequence alignment there are state transmissions

Emission count : 10

For insert state: 1

Transition count:6

Probability is 1/6 match insert and hidden state is 1/30

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