Incorporating Background Distribution
Instead of using log-likelihood values in the PWM, as described in the previous paragraph, several methods uses log-odds scores in the PWMs. An element in a PWM is then calculated as, where is the probability of observing symbol i at position j of the motif, and is the probability of observing the symbol i in a background model. The PWM score then corresponds to the log-odds of the substring being generated by the motif versus being generated by the background, in a generative model of the sequence.
Read more about this topic: Position-specific Scoring Matrix
Famous quotes containing the words background and/or distribution:
“In the true sense one’s native land, with its background of tradition, early impressions, reminiscences and other things dear to one, is not enough to make sensitive human beings feel at home.”
—Emma Goldman (1869–1940)
“Classical and romantic: private language of a family quarrel, a dead dispute over the distribution of emphasis between man and nature.”
—Cyril Connolly (1903–1974)