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.
Published Version
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