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:
“Silence is the universal refuge, the sequel to all dull discourses and all foolish acts, a balm to our every chagrin, as welcome after satiety as after disappointment; that background which the painter may not daub, be he master or bungler, and which, however awkward a figure we may have made in the foreground, remains ever our inviolable asylum, where no indignity can assail, no personality can disturb us.”
—Henry David Thoreau (1817–1862)
“The question for the country now is how to secure a more equal distribution of property among the people. There can be no republican institutions with vast masses of property permanently in a few hands, and large masses of voters without property.... Let no man get by inheritance, or by will, more than will produce at four per cent interest an income ... of fifteen thousand dollars] per year, or an estate of five hundred thousand dollars.”
—Rutherford Birchard Hayes (1822–1893)