The utilization of parallel processing in bioinformatics is a relatively new development, and wide spread use of parallel processing in this domain has been limited by the availability of applications that exploit parallel architectures, as well as a historic lack of IT training in the life sciences. Presented is an evaluation of several computing clusters using two different gene sequence search applications capable of utilizing a parallel processing architecture (ParAlign and mpiBLAST). The objective of the study is to evaluate the utility of these dedicated gene searching applications (developed for parallel computing architectures) on different parallel computing systems. Results demonstrate the performance variability between parallel processing systems, as well as the differences between gene sequence searching applications in a cluster computing environment.