Abstract
The paper presents the novel highly efficient method to compare two symbol sequences free from alignment methodology and having no free parameters; the method is illustrated with several classic bioinformatics problems. The method is based on a convolution calculation of two binary sequences; these latter are specially derived from nucleotide symbol sequences. The approach could be implemented for a comparison of symbol sequences from any finite alphabet. The convolution computation is based on fast Fourier transform. The method allows a coarse grained parallelism. Here we show MPI technology implementation to the parallelism of the computations. Some estimations for efficiency of the method followed from parallelism implementation are provided and discussed.
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