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We proposed a LanLinux-based cloud system for ClustalW-MPI, a parallel implementation of Clustal-W based on MPI, where researchers can submit their sequence data online for multiple sequence alignment. ClustalW is one of the most widely used programs for multiple sequence alignment (MSA) in bioinformatics. However, current in-silico environmental conditions for MSAs are facing computing power problems. The proposed system uses the MPICH2 (a standard message-passing interface for distributed-memory applications used in parallel computing) for handling all the tasks associated with the multiple sequence alignment on the Web. It provides sufficient computing power for aligning large number of sequences at a time, with real-time monitoring capabilities to ensure correctness, efficiency and effectiveness.