A workflow for accelerated evolutionary analysis of genetic sequences
DOI:
https://doi.org/10.59681/2175-4411.v16.iEspecial.2024.1295Keywords:
Big Data, Genetic Distance, WorkflowAbstract
By nature, viruses are constantly mutating. Although most mutations do not change the behavior of a virus, some of these mutations can generate new variants, which, for example, can make a virus spread more quickly. One way to verify this evolution is through evolutive models. Therefore, the objective of this work is to evaluate the genetic evolution of viruses. The method used is pairwise alignment of the virus sequences, followed by calculation of genetic distance. Furthermore, to allow the evaluation of a large amount of sequence, these two steps are implemented through a Workflow. Results obtained through two case studies using the SARS-COV-2 and monkeypox viruses, showed not only the excellent performance of the workflow, considerably reducing the analysis execution time, but also the evolution of their genetic sequences.
Downloads
References
Farahat RA, Sah R, El-Sakka AA, others. Human monkeypox disease (MPX). Infez Med. 2022; 30: p. 372-391.
Hu B, Guo H, Zhou P, others. Characteristics of SARS-CoV-2 and COVID-19. Nature Reviews Microbiology. 2021; 19: p. 141-154.
Duffy S. Why are RNA virus mutation rates so damn high? PLOS Biology. 2018 August; 16: p. 1-6.
Verli H. Bioinformática: da Biologia à Flexibilidade Molecular. 1st ed.: Sociedade Brasileira de Bioquímica e Biologia Molecular - SBBq; 2014.
Junior MJ, Sena A, Rebello V. Fragmentando o DNA de Ferramentas de Alinhamento Progressivo: uma Metaferramenta Eficiente. Anais do XXIV Simp. em Sist. Comp. de Alto Desempenho; 2023; Porto Alegre, Brasil. p. 349–360.
Dezordi FZ, Neto AMD, Campos TL, Jeronimo PMC, Wallau GL. ViralFlow: A Versatile Automated Workflow for SARS-CoV-2 Genome Assembly, Lineage Assignment, Mutations and Intrahost Variant Detection. Viruses. 2022; 14: p. 217.
Kim K, Park K, Lee S, Baek SH, Lim TH, Kim J, et al. VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing. Bioinformatics. 2023 May; 39: p. btad293.
Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nature Biotechnology. 2017; 35: p. 316–319.
De O. Sandes EF, Miranda G, Martorell X, Ayguade E, Teodoro G, De Melo ACMA. MASA: A Multiplatform Architecture for Sequence Aligners with Block Pruning. ACM Trans. Parallel Comput. 2016; 2 (4): p. 1-31.
Downloads
Published
How to Cite
Issue
Section
License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
