Sequence analysis of biological samples with intermediate bleaching fluorescent signals.

A method of detecting multiple targets in a biological sample comprising: (a) contacting the sample with a first probe; (B) physically binding the first probe to a first target; (C) observing a first signal from the first probe; (D) applying a chemical agent comprising a base, a nucleophile or an oxidizing agent to modify the first signal; (E) contacting the sample with a second probe; (F) physically binding the second probe to a second target; and (g) observing a second signal from the second probe;