Patent ID: 7133781

Claim:
A method for determining a probablity that a set of biopolymer sequences is a member of a hidden Markov model (HMM) of a set of known biopolymer sequences comprising the steps of: a) constructing said HMM by 1) identifying at least two regions in the set of known biopolymer sequences and determining a state of matching for each region using scoring matrices, wherein at least one state of matching is similarity and at least one state of matching is dissimilarity: 2) producing modules for each of said match states from one or more nodes linked in order, wherein each node represents a distribution of monomers at corresponding positions in the sequences of said set of known biopolymer sequence; 3) linking said modules in the order in which regions occur to form the HMM; b) comparing a second set of biopolymer sequences to said HMM by evaluating the scoring matrices for the second set of biopolymer sequences to produce an output score that is the probability that the second set of biopolymer sequences is member of the HMM; and c) outputting said score.