20D-dynamic Representation of Protein Sequences

Authors

  • Agata Czerniecka* Medical University of Gdańsk
  • Dorota Bielińska-Wąż Medical University of Gdańsk
  • Piotr Wąż Medical University of Gdańsk

DOI:

https://doi.org/10.11145/cb.v3i1.610

Abstract

A new method of comparison of protein sequences called by us "20D-dynamic Representation of Protein Sequences" is presented [1]. 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.

[1] A. Czerniecka, D. Bielinska-Waz, P. Waz, T. Clark, 20D-dynamic representation of protein sequences, Genomics 107 (2016) 16--23.

Author Biographies

Agata Czerniecka*, Medical University of Gdańsk

Department of Radiology Informatics and Statistics, PhD studentВ 

В 

Dorota Bielińska-Wąż, Medical University of Gdańsk

Department of Radiological Informatics and Statistics, assistant professor

Piotr Wąż, Medical University of Gdańsk

Department of Nuclear Medicine,В assistant professor

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Published

2016-03-22

Issue

Vol. 3 No. 1 (2016)

Section

Conference Contributions

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