Mapping sequence to feature vector using numerical representation of codons targeted to amino acids for alignment-free sequence analysis

Das, Jayanta Kumar; Sengupta, A. K.; Choudhury, Pabitra Pal; Roy, Swarup

doi:10.1016/j.gene.2020.145096

Cited by 15 publications

(12 citation statements)

References 54 publications

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“…The continuous replacement of the branches in the tree of life (clade) is the key characteristic of biodiversity ( Silvestro et al, 2015 ). The viral biodiversity could be addressed by phylogenetic studies by analyzing the nucleotide/ amino acid homology ( Das et al, 2021 ). Clades are the monophyletic groups of organisms that share a common ancestor along with all its lineal descendants.…”

Section: Discussionmentioning

confidence: 99%

Geographical and temporal distribution of SARS-CoV-2 globally: An attempt to correlate case fatality rate with the circulating dominant SARS-CoV-2 clades

Sarkar

Chawla‐Sarkar

Majumdar

et al. 2021

Preprint

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Uncontrolled high transmission is driving the continuous evolution of SARS-CoV-2, leading to the nonstop emergence of the new variants with varying sensitivity to the neutralizing antibodies and vaccines. We have analysed of 8,82,740 SARS-CoV-2 genome sequences, collected and sequenced during late December 2019 to 25 March 2021 from all across the world. The findings revealed differences in temporal and spatial distribution, and predominance of various clades/variants among six different continents.We found no clear association between the pathogenic potential of the various clades by comparing the case fatality rate (CFR) of 170 countries with the predominant SARS-CoV-2 clades in those countries, demonstrating the insignificance of the clade specific mutations on case fatality. Overall, relying on a large-scale dataset, this study illustrated the time-based evolution and prevalence of various clades /variants among different geographic regions. The study may help in designing continent specific vaccines in the future.

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Section: Discussionmentioning

confidence: 99%

Geographical and temporal distribution of SARS-CoV-2 globally: An attempt to correlate case fatality rate with the circulating dominant SARS-CoV-2 clades

Sarkar

Chawla‐Sarkar

Majumdar

et al. 2021

Preprint

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“…It is therefore important to analyze the impact of positional alteration of nucleotides in codon during mutation. To specify their impact during codon formation it is worthy to have distinct quantification of each nucleotide based on some specific criteria [17]. In this present study, we use Rumer's numerical representation of four nucleotides based on the number of hydrogen bonds in their chemical structures.…”

Section: Methodsmentioning

confidence: 99%

“…The maximum number of amino acids i.e. eleven (11) are fall under weak class. Unlike, previous attempts we are able to classify all the codons into three different classes.…”

Section: Classification Of Amino Acidsmentioning

confidence: 99%

Investigation of Codon Alternation Patterns in Genetic Diseases through Numerical Representation and Codon Classification

Sengupta¹,

Choudhury

Chakraborty

et al. 2020

Preprint

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Motivation: Alteration of amino acid is possible due to mutation in codons that could have a potential impact in a diseased condition. Effective mutation analysis can help to predict the fate of the diseased individual which can be validated later by in-vitro experimentations. It may also help an individual who is asymptomatic but having a particular genetic change for early detection and diagnosis during any terminal diseases. We try to investigate the codon alteration patterns and its impact during mutation for the genes known to be responsible for a particular disease.Results: For our current study, we consider neurodegenerative and monogenic diseases. We use numerical representation based on a determinative degree and classification of codons as well as amino acids into three different classes (Strong, Weak and Transition) for the analysis. Our analysis reveals that the strong class codons are highly mutated followed by weak and transition class. We observe that most of the mutations occur in the first or second positions in the codon rather than the third. While looking into the chemical properties of amino acid, we observe that amino acids belong to the aliphatic group are affected most during missense mutations. Our investigation further emphasises that in most of the cases the change in the determinative degree of codon due to mutation is directly proportional to the physical density property. In addition, our scheme gives a more microscopic and alternative representation of the existing codon table that helps in deciphering interesting codon alteration patterns during mutations in disease pathogenesis.

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“…Then it uses a sequence mining tool to compute the local similarity. Das et al [23] developed a mapping sequence to feature vector using a numerical representation of codons targeted to amino acids for alignment-free sequence analysis. Bandyopadhyay [24] proposes another feature extraction strategy that employs a 1-gram algorithm for feature encoding.…”

Section: Introductionmentioning

confidence: 99%

“…Bharill et al [30] developed an approach to extract six-dimensional numerical feature vectors from a protein sequence. Likewise, many feature extraction techniques [23,20,24,31,25,30,28] have been introduced in the past, but, none of them is scalable. A scalable approach for selecting statistically relevant characteristics from a large sequence is required.…”

Section: Introductionmentioning

confidence: 99%

A Novel Scalable Apache Spark Based Feature Extraction Approaches for Huge Protein Sequence and their Clustering Performance Analysis

Jha¹,

Tiwari²,

Bharill³

et al. 2022

Preprint

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Genome sequencing projects are rapidly increasing the number of high-dimensional protein sequence datasets. Clustering a high-dimensional protein sequence dataset using traditional machine learning approaches poses many challenges. Many different feature extraction methods exist and are widely used. However, extracting features from millions of protein sequences becomes impractical because they are not scalable with current algorithms. Therefore, there is a need for an efficient feature extraction approach that extracts significant features.

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Mapping sequence to feature vector using numerical representation of codons targeted to amino acids for alignment-free sequence analysis

Cited by 15 publications

References 54 publications

Geographical and temporal distribution of SARS-CoV-2 globally: An attempt to correlate case fatality rate with the circulating dominant SARS-CoV-2 clades

Geographical and temporal distribution of SARS-CoV-2 globally: An attempt to correlate case fatality rate with the circulating dominant SARS-CoV-2 clades

Investigation of Codon Alternation Patterns in Genetic Diseases through Numerical Representation and Codon Classification

A Novel Scalable Apache Spark Based Feature Extraction Approaches for Huge Protein Sequence and their Clustering Performance Analysis

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