Patent ID: 7563576

Claim:
A method of determining the location of a decoding sequence on an array, said method comprising the steps of: a) providing an array substrate comprising individual sites, wherein a first and second subpopulation of identifier nucleic acids are distributed among said individual sites, said first and second subpopulation of identifier nucleic acids comprising the same primer sequence and a different decoding sequence adjacent to said primer sequence; b) providing a set of combinatorial decoding probes comprising a priming sequence complementary to said primer sequence and a variable region adjacent to said priming sequence, wherein said variable region comprises at least one decoding nucleotide that will basepair with a nucleotide of at least one of said different decoding sequences, wherein said set of combinatorial decoding probes comprises subsets, each subset having a different decoding nucleotide at the same position and a label unique to each different decoding nucleotide; and c) adding to said array substrate a subset of said set of combinatorial decoding probes and detecting the presence of said label, thereby determining the location of said decoding sequence on said array.