Hardware customization for scientific applications has shown a big potential for reducing power consumption and increasing performance. In particular, the automatic generation of ISA extensions for General-Purpose Processors (GPPs) to accelerate domain-specific applications is an active field of research. Those domain-specific customized processors are mostly evaluated in simulation environments due to technical and programmability issues while using real hardware. There is no automatic mechanism to test ISA extensions in a real hardware environment. In this paper we present a toolchain that can automatically identify candidate parts of the code suitable for acceleration to test them in a reconfigurable hardware. We validate our toolchain using a bioinformatic application, ClustalW, obtaining an overall speed-up over 2x.