Summary: Cloud computing is a very attractive alternative to get advantages of high performance data processing and easy management of the complex tools in a bioinformatics area. We present a method, in which computing resources such as existing PCs and small cluster systems can be utilized as private cloud computing infrastructure for an inter-query style of bioinformatics tools. We proposed a private cloud computing environment for bioinformatics applications of inter-processing tasks. Furthermore, we present a metadata repository schema and 6 query routing algorithms on it. We apply proposed algorithms to ClustalW, a multiple sequence alignment tool. Experimental result shows remarkable benefits in a proposed private cloud system in terms of performance and various user requirements.