Patent ID: 7906285

Claim:
A method to analyze nucleic acids comprising: (a) providing a random array of target nucleic acids, wherein the target nucleic acids are generated from multiple sources, and wherein each target nucleic acid is tagged with an identifier of the particular source of the nucleic acid and wherein each target nucleic acid comprises a first target domain and an adjacent second target domain; (b) contacting said array with: (i) a first probe set comprising: 1. a first probe pool comprising probes complementary to said first target domains; 2. a second probe pool comprising probes complementary to said second target domains; wherein at least one of said first and second probe pools comprises a label; (c) ligating probes from said first probe pool and probes from said second probe pool when hybridized to said first and second target domains to form first ligated probes; (d) detecting said first ligated probes to determine at least one nucleotide of said first target domain; (e) removing said first ligated probes; (f) repeating steps (b)-(e) to determine all nucleotides of said first target domain, wherein each nucleotide of said first target domain is determined multiple times, wherein nucleic acids from a particular source are recognized by the assigned tag sequence.