I am currently trying to understand the meme motif finder output and I have a little bit of an issue understanding what the bit score means when looking at the motifs:
If you look at the sample output, the y-axis on the motif is a bit-score.
As far as I know, the bit score is a metric for multiple alignments where it describes how much more searches you would have to perform until you find this alignment again.
Is this the same here ?
Does it define how many positions in my provided sequences you would have to search until you find this base?
The units are a measurement of information or certainty. Roughly speaking, the relative height is how certain you are to observe a particular residue or nucleotide at a particular position.
Randomness is maximum uncertainty — all events can happen with equal probability. The simplest case is flipping a fair coin and having equal chance to get a heads or tails.
The opposite of randomness is certainty — you expect some event to happen to the exclusion of most or all other possibilities, like when you roll a weighted die in a crooked casino run by Ricky Jay, and one face comes up more than all the others and makes the casino rich.
In the original paper on sequence logos by Crooks et al. they call the entropy measure at each base a measurement of conservation, which is defined as the difference between the uncertainty of what you observe in reality (which is low for one or two residues that you see more frequently than all others, such as in a transcription factor binding site), and the frequency you'd expect if the biology of where TFs bind was completely random (like some hypothetical factor that does its work without caring about the DNA sequence it binds to: you would have a pure 1-in-4 chance of seeing one of A, T, C, or G, at any position in the binding site).
High heights indicate high conservation/low uncertainty.
