Patent ID: 7734421

Claim:
A method for identifying a motif or a combination of motifs having a Boolean state of predetermined mutations in a set of sequences comprising: a) aligning a set of sequences of ordered motifs represented by a single-character code on a programmed computer using a multiple sequence alignment program, b) comparing a reference sequence with the set of sequences aligned in step (a) by forming a first numerical matrix A of dimensions N×M in which N designates a number of sequences and M designates a number of motifs of one sequence of said alignment, with value A i,j being equal to a first value A1 when the motif of position i of sequence j with a value ranging from 0 to N is mutated in relation to a motif of position i of the reference sequence and equal to a second value A2 in other cases, forming two analysis matrices B and C of mutations in which: matrix B is a matrix of unmutated couples, of couples which do not mutate simultaneously, of dimension M×M, value B i,k =B k,i being equal: to a first value B1 when A i,j =A k,j =A1 irrespective of the value of j ranging from 0 to N, to a second value B2 in other cases; matrix C is a matrix of mutated couples of dimension M×M, value C k,i =C i,k being equal: to a second value C1 when A i,j =A k,j irrespective, of the value of j ranging from 0 to N, to a first value C2 in other cases; determining for a set E of positions a coefficient R E whose value is R 1 when values B i,k are equal to a second value B2, irrespective of the values of i and k belonging to set E of said positions, determining for a set F of positions, a coefficient R F , the value of which is R 1 when values C i,k are equal to second value C2, irrespective of the values of i and k belonging to set F of said positions; wherein in the matrices, i and k designate positions and j designates a sequence, and c) identifying motifs not having mutated simultaneously or motifs having mutated simultaneously at least once on at least one sequence of the set and not having mutated on another sequence of said set.