**0**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:

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! :)

**0**• written 2.4 years ago by jordidebruin •

**0**