A Novel Method for Alignment-free DNA Sequence Similarity Analysis Based on the Characterization of Complex Networks

Zhou, Jie; Zhong, Pianyu; Zhang, Tinghui

doi:10.4137/ebo.s40474

Cited by 11 publications

(5 citation statements)

References 30 publications

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“…For a graph, there are many measurements, such as graph energy ( Qi et al, 2011;Wu et al, 2015;Yu et al, 2017 ), Laplacian graph ene.g. ( Wu et al, 2015 ), spectral radius, point centrality ( Zhou et al, 2016 ), average degree of nodes ( Zhou et al, 2016 ) etc. They have been applied in sequence analysis successfully.…”

Section: Spectral Radius Of Graphmentioning

confidence: 99%

A novel model for protein sequence similarity analysis based on spectral radius

Gao

Marinis

et al. 2018

Journal of Theoretical Biology

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Advances in sequencing technologies led to rapid increase in the number and diversity of biological sequences, which facilitated development in the sequence research. In this paper, we present a new method for analyzing protein sequence similarity. We calculated the spectral radii of 20 amino acids (AAs) and put forward a novel 2-D graphical representation of protein sequences. To characterize protein sequences numerically, three groups of features were extracted and related to statistical, dynamics measurements and fluctuation complexity of the sequences. With the obtained feature vector, two models utilizing Gaussian Kernel similarity and Cosine similarity were built to measure the similarity between sequences. We applied our method to analyze the similarities/dissimilarities of four data sets. Both proposed models received consistent results with improvements when compared to that obtained by the ClustalW analysis. The novel approach we present in this study may therefore benefit protein research in medical and scientific fields.

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Section: Spectral Radius Of Graphmentioning

confidence: 99%

A novel model for protein sequence similarity analysis based on spectral radius

Gao

Marinis

et al. 2018

Journal of Theoretical Biology

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“…There exist many different alignment-free methods. For example, Zhou et al constructed a complex network for similarity/dissimilarity analysis of DNA sequences [ 1 ]. Saw et al perform DNA sequence comparison using the fuzzy integral with Markov chain [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

Non-standard bioinformatics characterization of SARS-CoV-2

Bielińska-Wąż

Wąż

2021

Computers in Biology and Medicine

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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. As the graphical representations of the sequences, the projections of the graphs into 2D and 3D spaces are used. The method has been applied to an analysis of the complete genome sequences of the 2019 novel coronavirus. As a result, 2D and 3D classification maps are obtained. The coordinate axes in the maps correspond to the values derived from the exact formulas characterizing the graphs: the coordinates of the centers of mass and the 4D moments of inertia. The points in the maps represent sequences and their coordinates are used as the classifiers. The main result of this work has been derived from the 3D classification maps. The distribution of clusters of points which emerged in these maps, supports the hypothesis that SARS-CoV-2 may have originated in bat and in pangolin. Pilot calculations for Zika virus sequence data prove that the proposed approach is also applicable to a description of time evolution of genome sequences of viruses.

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“…In bioinformatics, there are many different alignment-free methods. For example, Zhou et al constructed a complex network for similarity/dissimilarity analysis of DNA sequences [13]. We represented the protein sequence as a set of material points in a 20D space [14].…”

Section: G G T T G G a A 2 G T G T G A G Amentioning

confidence: 99%

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

Bielińska-Wąż

Wąż

Lass

et al. 2022

Life

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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 Echinococcus multilocularis in red foxes in Poland. Sequences of three mitochondrial genes, i.e., NADH dehydrogenase subunit 2 (nad2), cytochrome b (cob), and cytochrome c oxidase subunit 1 (cox1), are analyzed. The sequences are represented by sets of material points in a 4D space, i.e., 4D-dynamic graphs. As a visualization of the sequences, projections of the graphs into 3D space are shown. The differences between 3D graphs corresponding to European, Asian, and American haplotypes are small. Numerical characteristics (sequence descriptors) applied in the studies can recognize the differences. The concept of creating descriptors of 4D-dynamic graphs has been borrowed from classical dynamics; these are coordinates of the centers or mass and moments of inertia of 4D-dynamic graphs. Based on these descriptors, classification maps are constructed. The concentrations of points in the maps indicate one Polish haplotype (EmPL9) of Asian origin.

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A Novel Method for Alignment-free DNA Sequence Similarity Analysis Based on the Characterization of Complex Networks

Cited by 11 publications

References 30 publications

A novel model for protein sequence similarity analysis based on spectral radius

A novel model for protein sequence similarity analysis based on spectral radius

Non-standard bioinformatics characterization of SARS-CoV-2

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

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