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Biological sequence processing is a key of information technology for molecular biology. This scientific area requires powerful computing resources for exploring large sets of biological data. Multiple sequence alignment is an important method in the DNA and protein analysis. ClustalW has become the most popular tool and implements a progressive method for multiple sequence alignment. The goal of this paper is to propose the performance evaluation of the efficiency of parallel multiple alignment on the supercomputer BlueGene/P for the case study of investigating viral nucleotide sequences and finding out consensus motifs and variable domains in the different segments of influenza virus A genome. Parallel performance evaluation and profiling of multiple sequence alignment have been performed on the basis of parallel program implementation based on ClustalW method and a local mirror database of all available isolates of the 8 segments of the influenza virus A. The molecular biology outcome of the experiments is that the consensus and the variable domains in Influenza virus A under investigation have been determined and output by utilizing the biological sequence alignment editor UGENE UniPro.