The characterization of the security of embedded systems in 'black box' or 'gray box' against Side-Channel attacks often requires a preparatory phase of Reverse-Engineering, which can be particularly time-consuming, especially on a complex System-on-Chip that can be found in smartphones or in the automotive industry. This phase can, for example, consist of detecting a cryptographic primitive within Side-Channel measurements for a future observation attack, or a target routine for a fault injection attack. The objective of this thesis is to develop a methodology and non-profiled tools that allow the automation of this detection phase, while enabling the exploitation of prior knowledge of a potential attacker.