Sequence Motif - Motif Bioinformatics

Motif Bioinformatics

Consider the N-glycosylation site motif mentioned above:

Asn, followed by anything but Pro, followed by either Ser or Thr, followed by anything but Pro

This pattern may be written as N{P}{P} where N = Asn, P = Pro, S = Ser, T = Thr; {X} means any amino acid except X; and means either X or Y.

The notation does not give any indication of the probability of X or Y occurring in the pattern. Observed probabilities can be graphically represented using sequence_logos. Sometimes patterns are defined in terms of a probabilistic model such as a hidden Markov model.