Biologists require ways to rapidly sequence vast amounts of DNA information. An approach to satisfying the demand is to provide hardware support and leverage parallel computation. When providing hardware acceleration it is known that a custom specific circuit will provide a high performance solution. Providing a balance between delivering an application-specific circuit while achieving optimal utilization of a Field Programmable Gate Array is a difficult task. This paper presents a technique in which a custom circuit solution for a given parameter set is generated for the edit-distance problem in comparing two sequences for similarity.