Patent ID: 7403943

Claim:
A method for identifying patterns in a set of k-sequences of symbols, where k is greater than or equal to two, and wherein the location of a symbol in a sequence is denoted by a position index, the method comprising the steps of: (a) identifying a 2-tuple of patterns of symbols common to each pair-wise combination of sequences; (b) for each pattern of symbols in each identified 2-tuple of patterns, creating a position index numerical array (PINA) representing that pattern, each position index numerical array (PINA) comprising a set of position indices, each position index in the set denoting the location in a selected reference sequence at which each symbol in that pattern occurs; and (c) taking all 2-tuples that share a common reference sequence in pair-wise combination, (i) converting the position index numerical array (PINA) representing each of the patterns in one of the 2-tuples into a corresponding position index binary array (PIBA) representing that pattern, each position index binary array (PIBA) comprising a set of binary digits, the binary digit in each place in a position index binary array (PIBA) that corresponds to a location in the selected reference sequence of a symbol in a pattern being a first predetermined binary value, all other binary digits in the position index binary array (PIBA) being a second predetermined binary value; and (ii) using each position index in each position index numerical array (PINA) in the other 2-tuple to interrogate the places in the binary arrays of the first 2-tuple, thereby to identify those places in each binary array in the first 2-tuple having the first predetermined binary value.