Classification Maps: A New Mathematical Tool Supporting the Diagnosis of Age-Related Macular Degeneration.

Objective: A new diagnostic graphical tool-classification maps-supporting the detection of Age-Related Macular Degeneration (AMD) has been constructed.

Methods: The classification maps are constructed using the ordinal regression model. In the ordinal regression model, the ordinal variable (the dependent variable) is the degree of the advancement of AMD.

4D-Dynamic Representation of DNA/RNA Sequences: Studies on Genetic Diversity of in Red Foxes in Poland.

The 4D-Dynamic Representation of DNA/RNA Sequences, an alignment-free bioinformatics method recently developed by us, has been used to study the genetic diversity of in red foxes in Poland. Sequences of three mitochondrial genes, i.e.

Applications of 2D and 3D-Dynamic Representations of DNA/RNA Sequences for a Description of Genome Sequences of Viruses.

Unlabelled: The aim of the studies is to show that graphical bioinformatics methods are good tools for the description of genome sequences of viruses. A new approach to the identification of unknown virus strains, is proposed.

Methods: Biological sequences have been represented graphically through 2D and 3D-Dynamic Representations of DNA/RNA Sequences - theoretical methods for the graphical representation of the sequences developed by us previously.

Non-standard bioinformatics characterization of SARS-CoV-2.

A non-standard bioinformatics method, 4D-Dynamic Representation of DNA/RNA Sequences, aiming at an analysis of the information available in nucleotide databases, has been formulated. The sequences are represented by sets of "material points" in a 4D space - 4D-dynamic graphs. The graphs representing the sequences are treated as "rigid bodies" and characterized by values analogous to the ones used in the classical dynamics.

Spectral-dynamic representation of DNA sequences.

A graphical representation of DNA sequences in which the distribution of a particular base B=A,C,G,T is represented by a set of discrete lines has been formulated. The methodology of this approach has been borrowed from two areas of physics: spectroscopy and dynamics. Consequently, the set of discrete lines is referred to as the B-spectrum.

Characterizing the Zika Virus Genome - A Bioinformatics Study.

Background: The recent epidemic of Zika virus infections in South and Latin America have raised serious concern on its ramifications for the population in the Americas and spread of the virus worldwide. The Zika virus disease is a relatively new phenomenon for which sufficient and comprehensive data and investigative reports have not been available to date.

Objective: To carry out a bioinformatics study of the available Zika virus genomic sequences to characterize the virus.

20D-dynamic representation of protein sequences.

A new method of comparison of protein sequences has been formulated. The sequence of amino acids is 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.

Non-standard similarity/dissimilarity analysis of DNA sequences.

Similarity/dissimilarity analysis of DNA sequences is performed using 3D-dynamic representation. The sequences are represented by material points in a 3D-space. Descriptors related to such 3D-dynamic graphs are calculated.

3D-dynamic representation of DNA sequences.

A new 3D graphical representation of DNA sequences is introduced. This representation is called 3D-dynamic representation. It is a generalization of the 2D-dynamic dynamic representation.

Descriptors of 2D-dynamic graphs as a classification tool of DNA sequences.

A new tool of the classification of DNA sequences is introduced. The method is based on 2D-dynamic graphs and their descriptors. Using the descriptors created by centers of masses, moments of inertia, angles between the axis and the principal axis of inertia of the 2D-dynamic graphs one can obtain classification diagrams in which similar sequences are clustered in separated areas.

Graphical and numerical representations of DNA sequences: statistical aspects of similarity.

New approaches aiming at a detailed similarity/dissimilarity analysis of DNA sequences are formulated. Several corrections that enrich the information which may be derived from the alignment methods are proposed. The corrections take into account the distributions along the sequences of the aligned bases (neglected in the standard alignment methods).

Classification studies based on a spectral representation of DNA.

The aim of this paper is to provide a new tool to classify the nucleic acid sequences. The profiles based on the values characterizing DNA sequences (descriptors derived from recently introduced graphical representation) are used as a basis of classification schemes related to different aspects of similarity of the sequences. New multicomponent similarity measures based on these descriptors have been defined.