Matching Genetic Sequences in Distributed Adaptive Computing Systems

Distributed adaptive computing systems (ACS) allow developers to design applications using multiple programmable devices. The ACS API, an API created for distributed adaptive com-puting, gives developers the ability to design scalable ACS systems in a cluster networking environment for large applications. One such application, found in the field of bioinformatics, is the DNA sequence alignment problem. This thesis presents a runtime reconfigurable FPGA implementation of the Smith-Waterman similarity comparison algorithm. Additionally, this thesis presents tools designed for the ACS API that assist developers creating applications in a heterogeneous distributed adaptive computing environment.