Methods for reducing complexity of nucleic acid samples

A method of analyzing a subset of nucleic acids within a nucleic acid population, comprising:

• (a) providing a single-stranded driver population of nucleic acids and a single-stranded tester population of nucleic acids;
• (b) annealing said driver population of nucleic acids to said tester population of nucleic acids;
• (c) immobilizing said driver population of nucleic acids;
• (d) separating said unimmobilized subset of nucleic acids from said immobilized nucleic acids;
• (e) hybridizing said unimmobilized subset of nucleic acids to probes on a microarray;
• and
• (f) determining which of said probes on said microarray hybridize to said unimmobilized subset of nucleic acids, thereby analyzing said unimmobilized subset of nucleic acids.

A method of analyzing a subset of nucleic acids within a nucleic acid population, comprising:

• (a) providing a single-stranded driver population of nucleic acids and a single-stranded tester population of nucleic acids;
• (b) annealing said driver population of nucleic acids to said tester population of nucleic acids;
• (c) immobilizing said driver population of nucleic acids;
• (d) separating said unimmobilized nucleic acids from said immobilized nucleic acids;
• (e) dissociating tester nucleic acids annealed to immobilized driver nucleic acids to produce a subset of complementary tester nucleic acids;
• (f) separating said subset of complementary tester nucleic acids from said immobilized driver nucleic acids;
• (g) hybridizing said subset of complementary tester nucleic acids to probes on a microarray;
• (h) determining which of said probes on said microarray hybridize to said subset of complementary tester nucleic acids, thereby analyzing said subset of complementary tester nucleic acids.