Recently, the amount of genome sequence is increasing rapidly due to advanced computational techniques and experimental tools in the biological area. Sequence comparisons are very useful operations to predict the functions of the genes or proteins. However, it takes too much time to compare long sequence data and there are many research results for fast sequence comparisons. In this paper, we propose a hybrid grid system to improve the performance of the sequence comparisons based on the LanLinux system. Compared with conventional approaches, hybrid grid is easy to construct, maintain, and manage because there is no need to install SWs for every node. As a real experiment, we constructed an orthologous database for 89 prokaryotes just in a week under hybrid grid; note that it requires 33 weeks on a single computer.