Patent ID: 8738296

Claim:
A method of generating an index, the index operable to determine where, in a reference sequence, a data set of one or more related oligomer sequences maps to the reference sequence, the oligomer sequences of the data set obtained from a same fragment of genetic material, the method comprising: applying, with a computer system, a key pattern to the reference sequence to generate a plurality of keys, wherein the key pattern includes a first set of N contiguous positions separated by K positions from a second set of M contiguous positions, the separation being based on predicted relationships between oligomer sequences of the data set, wherein the key pattern is defined by predetermined values for N, K and M, the applying including: applying the key pattern to a first location of the reference sequence to obtain a first set of bases, the first set of bases including: N contiguous bases of the reference sequence starting from the first location, and M contiguous bases of the reference sequence starting from N+K positions after the first location, N, M, and K being integers greater than or equal to one; using the first set of bases to generate a first key; applying the key pattern to a plurality of other locations to generate other keys, wherein the applying of the key pattern to the first and other locations uses the same values for N, M, and K; and storing the keys in the index, the index being stored in a searchable computer readable medium; wherein each key corresponds to one or more possible locations within the reference sequence.