Negative score

[Tania Cid]

Hi,

What does mean to have a negative score when analyzing the binding of a TF motiff to a sequence?

Example:

Name: MA0137.3
Id: MA0137.3.STAT1
Score: -0.7407
Relative score: 0.7503
Seq: seq1
start: 318
end: 328
strand: +
sequence: GGCCTGGGAAG

Thanks in advance

[anthony....@gmail.com]

Hi Tania,

The score corresponds to the PWM score, which is the sum of positive and negative scores in the PWM used. These scores are obtained via log-likelihood ratios. I suggest you read the following paper to get more details: https://www.nature.com/articles/nrg1315