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. 1994 Dec;10(6):605-11.
doi: 10.1093/bioinformatics/10.6.605.

Multidimensional dot-matrices

V A Shepelev  1 , N V Yanishevsky
Affiliations

Multidimensional dot-matrices

V A Shepelev et al. Comput Appl Biosci. 1994 Dec.

Abstract

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 coordinates (xi, sigma j not equal to ixj/(n - 1)) are 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 of O[n*L2 + n*(L2p)2] is suggested 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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