Physics-Based Signal Analysis of Genome Sequences: An Overview of GenomeBits DOI Creative Commons
Enrique Canessa

Microorganisms, Journal Year: 2023, Volume and Issue: 11(11), P. 2733 - 2733

Published: Nov. 9, 2023

A comprehensive overview of the recent physics-inspired genome analysis tool, GenomeBits, is presented. This based on traditional signal processing methods such as discrete Fourier transform (DFT). GenomeBits can be used to extract underlying genomics features from distribution nucleotides, and further analyze mutation patterns in viral genomes. Examples main findings outlining intrinsic organization sequences for different SARS-CoV-2 variants along pandemic years 2020-2022 Monkeypox cases 2021 are presented show usefulness GenomeBits. results DFT genomes geographical regions discussed, together with complete first coronavirus reported: Alpha, Beta, Gamma, Epsilon Eta. Interesting Delta Omicron form a unique 'order-disorder' transition uncovered these samples, well their cumulative function scatter plots. class transitions might reveal outcome mutations spike protein. salient feature mapping nucleotide bases (A,T,C,G) into an alternating spin-like numerical sequence via series having binary (0,1) indicators each A,T,C,G. leads derivation set statistical curves. Furthermore, quantum-based extension model analogous probability measure shown identify properties wavefunctions superposition states. An association integral coding binding-like energy can, principle, also established. The relevance bioinformatics analyzed.

Language: Английский

Evolution of Sequence and Structure of SARS-CoV-2 Spike Protein: A Dynamic Perspective DOI Creative Commons

Anushree Sinha,

Satyam Sangeet, Susmita Roy

et al.

ACS Omega, Journal Year: 2023, Volume and Issue: 8(26), P. 23283 - 23304

Published: June 21, 2023

Novel coronavirus (SARS-CoV-2) enters its host cell through a surface spike protein. The viral protein has undergone several modifications/mutations at the genomic level, which it modulated structure–function and passed variants of concern. Recent advances in high-resolution structure determination multiscale imaging techniques, cost-effective next-generation sequencing, development new computational methods (including information theory, statistical methods, machine learning, many other artificial intelligence-based techniques) have hugely contributed to characterization sequence, structure, function proteins, different understand pathogenesis, evolutions, transmission. Laying on foundation sequence–structure–function paradigm, this review summarizes not only important findings structure/function but also structural dynamics components, highlighting effects mutations them. As dynamic fluctuations three-dimensional often provide clues for functional modulation, quantifying time-dependent mutational events over genetic/amino acidic sequence helps identify alarming transitions having implications enhanced fusogenicity pathogenicity virus. Although these are more difficult capture than static, average property, encompasses those challenging aspects characterizing evolutionary their functions.

Language: Английский

Citations

9
GenomeBits Characterization of MPXV DOI Open Access
Enrique Canessa

Genes, Journal Year: 2022, Volume and Issue: 13(12), P. 2223 - 2223

Published: Nov. 27, 2022

Genome sequences of the monkeypox virus (MPXV) causing current outbreak are being reported from an increasing number countries. We present a letter-to-numerical sequence study via GenomeBits signal mapping in order to characterize evolution MPXV simple statistical analysis. Histograms, empirical and theoretical cumulative distribution curves resulting scatter plots for base nucleotides A C versus their complementary T G discussed. may help surveillance emergent infectious diseases.

Language: Английский

Citations

3
Physics-Based Signal Analysis of Genome Sequences: An Overview of GenomeBits DOI Creative Commons
Enrique Canessa

Microorganisms, Journal Year: 2023, Volume and Issue: 11(11), P. 2733 - 2733

Published: Nov. 9, 2023

A comprehensive overview of the recent physics-inspired genome analysis tool, GenomeBits, is presented. This based on traditional signal processing methods such as discrete Fourier transform (DFT). GenomeBits can be used to extract underlying genomics features from distribution nucleotides, and further analyze mutation patterns in viral genomes. Examples main findings outlining intrinsic organization sequences for different SARS-CoV-2 variants along pandemic years 2020-2022 Monkeypox cases 2021 are presented show usefulness GenomeBits. results DFT genomes geographical regions discussed, together with complete first coronavirus reported: Alpha, Beta, Gamma, Epsilon Eta. Interesting Delta Omicron form a unique 'order-disorder' transition uncovered these samples, well their cumulative function scatter plots. class transitions might reveal outcome mutations spike protein. salient feature mapping nucleotide bases (A,T,C,G) into an alternating spin-like numerical sequence via series having binary (0,1) indicators each A,T,C,G. leads derivation set statistical curves. Furthermore, quantum-based extension model analogous probability measure shown identify properties wavefunctions superposition states. An association integral coding binding-like energy can, principle, also established. The relevance bioinformatics analyzed.

Language: Английский

Citations

0