Cyanine dyes are used for both nucleic acid and protein labeling for visualization and quantification purposes. Biological applications include comparative genomic hybridization and gene chips, which are used in transcriptomics, and various studies in proteomics such as RNA localization, molecular interaction studies by fluorescence energy transfer (FRET) and fluorescent immunoassays.

Cy5 is fluorescent in the red region (~650 excitation, 670 nm emission).