20D-dynamic Representation of Protein Sequences
A new method of comparison of protein sequences called by us "20D-dynamic Representation of Protein Sequences" is presented . This method belongs to the group of alignment-free methods. This class of methods constitute a fast developing branch of bioinformatics. The alignment-free methods reveal different aspects of similarity with low computational effort. They offer both numerical and graphical tools for sequence comparisons. In the 20D-dynamic Representation of Protein Sequences, the sequences of amino acids are represented by a set of point masses in a 20D space. The distribution of points in the space is obtained by applying the method of "a walk" in the 20D space. As a consequence a 20D-dynamic graph is obtained which is a mathematical representation of the protein sequence. The 3D and 2D projections of this graph are convenient graphical tools for sequence comparison. The descriptors, i.e. the numerical values characterizing the 20D-dynamic graphs, are designed using the ideas coming from the classical dynamics (moments of inertia of rigid bodies). Some numerical examples of this method, using NADH dehydrogenase subunit 5 (ND5) protein sequences of nine species and subunit 6 (ND6) of eight species, are presented.
 A. Czerniecka, D. Bielinska-Waz, P. Waz, T. Clark, 20D-dynamic representation of protein sequences, Genomics 107 (2016) 16--23.
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