Question: How to calculate the Position Weight Matrix score?
0
gravatar for jordidebruin
5 months ago by
jordidebruin0 wrote:

Hi,

Can anyone explain me how to calculate the Position Weight Matrix score?

I know the formula, but I don't understand it. I have a table with the frequences of nucleotides, and a table with the PWM scores:

Frequences of nucleotides:

Position:            1       2        3        4        5

A                    0       0.9      0.1      0.6      0.2
C                    0       0        0.2      0.1      0.2
G                    0       0        0.1      0        0.1
T                    1       0.1      0.6      0.3      0.5

And I have the corresponding PWM scores:

Position:            1       2        3        4         5

A                            1.848   -1.322    1.263    -0.322
C                                    -0.322   -1.322    -0.322
G                                    -1.322             -1.322
T                    1      -1.322    1.263    0.263     1

But, I have no idea how this scores are calculated. The formula is:

enter image description here

But I don't understand this.

Can anyone explain me step by step how I can calculate this scores?

I especially don't understand how to calculate p(b,i).

Thanks! :)

score pssm pwm bioinformatics • 467 views
ADD COMMENTlink modified 5 months ago by Santosh Anand2.9k • written 5 months ago by jordidebruin0
3
gravatar for Santosh Anand
5 months ago by
Santosh Anand2.9k
Santosh Anand2.9k wrote:

p(b) = expected background frequency of each nucleotides. You can assume it to be 0.25 (4 nucleotides distributed uniformly in background).

p(b, i) is the frequency of the corresponding row and column. Example:

Pos 2A: PWM = log2(0.9/0.25)

Pos 2T = log2(0.1/0.25)

Basically, you have to divide the frequency matrix by 0.25 (the background frequency of each nucleotide) and take the log2 of result.

ADD COMMENTlink modified 5 months ago • written 5 months ago by Santosh Anand2.9k

Thank you very much!! Now I understand it.

ADD REPLYlink written 5 months ago by jordidebruin0
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