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© Oxford University Press

Multidimensional dot-matrices

V.A. Shepelev and N.V. Yanishevsky

Institute of Molecular Genetics, Russian Academy of Sciences Kurchatov Square, Moscow 123182, Russia

A generalization of the dot-matrix of similarity for n sequences is proposed. For the visualization of the n-dimensional dot-matrix, the n projections onto the plane passing through the main diagonal and each of the n axes of Euclidean space En are displayed. The projection is compressed so that the points at the coordinatesare depicted on the plane. The common regions of similarity are revealed as segments of straight lines parallel to the main diagonal. An algorithm for the n-dimensional dot-matrix calculation of time of the order ofsuggested where L is the mean length of sequence and p is the stringency parameter of the order of 10–6. The method is illustrated for the family of plant phenylalanine ammonia-lyase genes.


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