Entering edit mode
6.7 years ago
bharata1803
▴
560
Hello,
So, I use FIMO for calculating PWM score for a sequence.
How does FIMO calculate the score actually? It says it is the log likelihood of the PWM given background.
Can anyone give step by step? Suppose I have PWM:
A C G T
1 0.2 0.4 0.4 0
2 0.4 0.2 0.4 0
3 0.6 0 0.2 0.2
4 0 1 0 0
5 1 0 0 0
6 0 0 0.8 0.2
7 0 0.2 0.8 0
8 0 0 0 1
9 0 0 1 0
10 0 0.2 0.4 0.4
11 0 0.4 0 0.6
12 0.2 0 0.6 0.2
And sequence: GGGCAGCTGGCA And background:
A 0.275
C 0.225
G 0.275
T 0.225
FIMO score is: 10.8211
This answer explains it well.