A distributed approach for a multiple sequence alignment algorithm using a parallel virtual machine

Multiple sequence alignment is a central topic of extensive research in computational biology. Basically, two or more protein sequences are compared so as to evaluate their similarity. This work reports a methodology for parallel processing of a multiple sequence alignment algorithm (ClustalW) in an environment of networked computers. A detailed description of the modules that compose the distributed system is provided, giving special attention to the way a dynamic programming algorithm can be executed in parallel. Extensive experiments were done to evaluate performance and scalability of the method. Results show that the proposed method is efficient and offers a real advantage for large-scale multiple protein sequence alignment.