Question: Meme-Tools: Bit score
0
gravatar for chrys
9 weeks ago by
chrys30
Germany
chrys30 wrote:

Hi guys,

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:

http://meme-suite.org/doc/examples/meme_example_output_files/meme.html

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?

Thanks for any help you can offer !

bit score alignment meme • 163 views
ADD COMMENTlink modified 9 weeks ago by Alex Reynolds22k • written 9 weeks ago by chrys30
1
gravatar for Alex Reynolds
9 weeks ago by
Alex Reynolds22k
Seattle, WA USA
Alex Reynolds22k wrote:

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.

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by Alex Reynolds22k
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