Multidimensional dot-matrices.
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.
Shepelev
V A
VA
Institute of Molecular Genetics, Russian Academy of Sciences, Moscow.
Yanishevsky
N V
NV
D000465:Algorithms; D008838:Microcomputers; D010650:Phenylalanine Ammonia-Lyase / Q000235:genetics; D011336:Probability; D016415:Sequence Alignment / Q000379:methods*; D017386:Sequence Homology, Amino Acid
D010650:Phenylalanine Ammonia-Lyase