Patent ID: 8738299

Claim:
A method for finding a gene in a DNA sequence (S), said gene represented by an ordered set of M distinct marker strings m 1 , m 2 , . . . , m m , said M at least 3, said method comprising the steps of: for i=1, 2, . . . , M, identifying a sub-string V i in S, wherein sub-string V i consists of J identical elements V ij (j=1, 2, . . . , J) such that V ij specifies a sequential position number P j in S at which m i is located in S, wherein each identical element V ij in V i consists of m i , wherein V ij are ordered in sub-string V i such that P 1 <P 2 , . . . <P J , wherein J is a function of i, and wherein J is at least 2 for each i; for each sub-string V i (i=1, 2, . . . , M−1), a processor of a computer system creating a plurality of directed links from specific elements of sub-string V i to specific elements of sub-string V i+1 , subject to said directed links satisfying a same inter-marker length constraint for each directed link; said processor tracing all paths that connect sub-string V 1 to sub-string V M using said directed links, wherein said paths satisfy a sequence length constraint; and storing said traced paths in a storage device of a computer system, wherein said same inter-marker length constraint is selected from the group consisting of a difference between a position number within the set of specific elements of V i and a position number within the set of specific elements of V i+1 for each directed link being a specified constant value, a difference between a position number within the set of specific elements of V i and a position number within the set of specific elements of V i+1 for each directed link being less than a specified constant value, and a difference between a position number within the set of specific elements of V i and a position number within the set of specific elements of V i+1 for each directed link being more than a specified constant value, and wherein each specified constant value differs from zero.