A new graph-theoretic approach to determine the similarity of genome sequences based on nucleotide triplets

Das, Subhram; Das, Arijit; Bhattacharya, D. K.; Tibarewala, D. N.

doi:10.1016/j.ygeno.2020.08.023

Cited by 13 publications

(8 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It can be grouped into five clusters; namely H1N1 (blue), H2N2 (pink), H5N1 (red), H7N9 (black), and H7N3 (green). Our result is compared with the results in (Das et al 2020a ), (Sims et al 2009 ), (Dong et al 2019 ). The phylogenetic tree constructed by the Graph-theoretic method (Das et al 2020a ) shows one misclassification where A/Turkey/VA/505472–18/2007 (H5N1) (red) is placed in the cluster of H1N1 (blue).…”

Section: Results Analysissupporting

confidence: 58%

“…The phylogenetic trees are constructed for these datasets using the UPGMA/NJ clustering method in MEGA11. The results from these datasets are compared with those of the formerly published methods that include the tri-nucleotide representation using J/J matrix method (Das et al 2018a ), the Graph-theoretic method (Das et al 2020a ), the Feature Frequency Profiles (FFP) method (Sims et al 2009 ), the Fuzzy Integral Similarity (FIS) method (Saw et al 2019 ), the Positional Correlation Natural Vector (PCNV) method (He et al 2020 ), the Multiple Encoding Vector (MEV) method (Li et al 2017 ), the Accumulated Natural Vector (ANV) method (Dong et al 2019 ). In most of the cases, it is observed that the appropriateness of the present results is better or equal to the results of the prior methods.…”

Section: Results Analysismentioning

confidence: 99%

“…The method is tested on several species of mammals, influenza-A viruses, ebola viruses, hepatitis C viruses and SARS-CoV-2 viruses. The results of the proposed method are compared with those of the existing methods like the tri-nucleotide representation using J/J matrix method (Das et al 2018a ), the Graph-theoretic method (Das et al 2020a ), the Feature Frequency Profiles (FFP) method (Sims et al 2009 ), the Fuzzy Integral Similarity (FIS) method (Saw et al 2019 ), the Positional Correlation Natural Vector (PCNV) method (He et al 2020 ), the Multiple Encoding Vector (MEV) method (Li et al 2017 ), and the Accumulated Natural Vector (ANV) method (Dong et al 2019 ), where the results are found to be highly satisfactory. The advantage of this method is that it is computationally fast, and it does not use any additional parameters to align genome sequences evenly, as is the case with traditional alignment-based methods.…”

Section: Discussionmentioning

confidence: 99%

“…Now, various attempts have been made by the authors on Graph-theoretic approaches (Qi et al 2011 ; Mathur and Adlakha 2016 ). The method described in (Das et al 2020a ) is quite prominent where only a complete bipartite graph defines a codons based genome sequence. Accordingly, a vector descriptor is formed using the weights of the edges of the graph.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Biochemical Property Based Positional Matrix: A New Approach Towards Genome Sequence Comparison

Dey¹,

Das²,

Bhattacharya

2022

J Mol Evol

Self Cite

View full text Add to dashboard Cite

The growth of the genome sequence has become one of the emerging areas in the study of bioinformatics. It has led to an excessive demand for researchers to develop advanced methodologies for evolutionary relationships among species. The alignment-free methods have been proved to be more efficient and appropriate related to time and space than existing alignment-based methods for sequence analysis. In this study, a new alignment-free genome sequence comparison technique is proposed based on the biochemical properties of nucleotides. Each genome sequence can be distributed in four parameters to represent a 21-dimensional numerical descriptor using the Positional Matrix. To substantiate the proposed method, phylogenetic trees are constructed on the viral and mammalian datasets by applying the UPGMA/NJ clustering method. Further, the results of this method are compared with the results of the Feature Frequency Profiles method, the Positional Correlation Natural Vector method, the Graph-theoretic method, the Multiple Encoding Vector method, and the Fuzzy Integral Similarity method. In most cases, it is found that the present method produces more accurate results than the prior methods. Also, in the present method, the execution time for computation is comparatively small.

show abstract

Section: Results Analysissupporting

confidence: 58%

Section: Results Analysismentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Biochemical Property Based Positional Matrix: A New Approach Towards Genome Sequence Comparison

Dey¹,

Das²,

Bhattacharya

2022

J Mol Evol

Self Cite

View full text Add to dashboard Cite

show abstract

“…Of note, some synonymous codons are preferentially selected over others at higher frequencies, resulting in synonymous codon usage bias, and is found in almost all available genomes. This biased synonymous codon usage is not neutral but involved in nucleotide usage bias (72,73), mRNA stability (74, 75), translation accuracy, efficiency (76,77), and protein folding formation (78).…”

Section: Discussionmentioning

confidence: 99%

Evolutionary dynamics of codon usages for peste des petits ruminants virus

Wang

Sun²,

Lu³

et al. 2022

Front. Vet. Sci.

View full text Add to dashboard Cite

Peste des petits ruminants virus (PPRV) is an important agent of contagious, acute and febrile viral diseases in small ruminants, while its evolutionary dynamics related to codon usage are still lacking. Herein, we adopted information entropy, the relative synonymous codon usage values and similarity indexes and codon adaptation index to analyze the viral genetic features for 45 available whole genomes of PPRV. Some universal, lineage-specific, and gene-specific genetic features presented by synonymous codon usages of the six genes of PPRV that encode N, P, M, F, H and L proteins reflected evolutionary plasticity and independence. The high adaptation of PPRV to hosts at codon usages reflected high viral gene expression, but some synonymous codons that are rare in the hosts were selected in high frequencies in the viral genes. Another obvious genetic feature was that the synonymous codons containing CpG dinucleotides had weak tendencies to be selected in viral genes. The synonymous codon usage patterns of PPRV isolated during 2007–2008 and 2013–2014 in China displayed independent evolutionary pathway, although the overall codon usage patterns of these PPRV strains matched the universal codon usage patterns of lineage IV. According to the interplay between nucleotide and synonymous codon usages of the six genes of PPRV, the evolutionary dynamics including mutation pressure and natural selection determined the viral survival and fitness to its host.

show abstract

Nucleotide and codon usage biases involved in the evolution of African swine fever virus: A comparative genomics analysis

Wang

Yang

et al. 2023

J Basic Microbiol

View full text Add to dashboard Cite

Since African swine fever virus (ASFV) replication is closely related to its host's machinery, codon usage of viral genome can be subject to selection pressures. A better understanding of codon usage can give new insights into viral evolution. We implemented information entropy and revealed that the nucleotide usage pattern of ASFV is significantly associated with viral isolation factors (region and time), especially the usages of thymine and cytosine. Despite the domination of adenine and thymine in the viral genome, we found that mutation pressure alters the overall codon usage pattern of ASFV, followed by selective forces from natural selection.Moreover, the nucleotide skew index at the gene level indicates that nucleotide usages influencing synonymous codon bias of ASFV are significantly correlated with viral protein hydropathy. Finally, evolutionary plasticity is proved to contribute to the weakness in synonymous codons with A-or T-end serving as optimal codons of ASFV, suggesting that finetuning translation selection plays a role in synonymous codon usages of ASFV for adapting host. Taken together, ASFV is subject to evolutionary dynamics on nucleotide selections and synonymous codon usage, and our detailed analysis offers deeper insights into the genetic characteristics of this newly emerging virus around the world.

show abstract

A new graph-theoretic approach to determine the similarity of genome sequences based on nucleotide triplets

Cited by 13 publications

References 50 publications

Biochemical Property Based Positional Matrix: A New Approach Towards Genome Sequence Comparison

Biochemical Property Based Positional Matrix: A New Approach Towards Genome Sequence Comparison

Evolutionary dynamics of codon usages for peste des petits ruminants virus

Nucleotide and codon usage biases involved in the evolution of African swine fever virus: A comparative genomics analysis

Contact Info

Product

Resources

About