Due to the ever increasing amounts of data in application areas relevant both for business and research, the requirements for data handling have increased significantly over the last years, often exceeding the capabilities of standard software, which has been used in specific application areas. To face this challenges software needs to be adapted or rewritten to integrate novel big data handling techniques. This paper focuses on the implementation of a genome sequence comparison application from the domain of bioinformatics running on top of Hadoop while relying on HBase for data management and MapReduce jobs for computation.