Evaluation of genome similarities using a wavelet-domain approach
Rev. Soc. Bras. Med. Trop
; 53: e20190470, 2020. tab, graf
Artigo
em Inglês
| Sec. Est. Saúde SP, Coleciona SUS, LILACS
| ID: biblio-1136864
Biblioteca responsável:
BR1.1
ABSTRACT
Abstract INTRODUCTION:
Tuberculosis is listed among the top 10 causes of deaths worldwide. The resistant strains causing this disease have been considered to be responsible for public health emergencies and health security threats. As stated by the World Health Organization (WHO), around 558,000 different cases coupled with resistance to rifampicin (the most operative first-line drug) have been estimated to date. Therefore, in order to detect the resistant strains using the genomes of Mycobacterium tuberculosis (MTB), we propose a new methodology for the analysis of genomic similarities that associate the different levels of decomposition of the genome (discrete non-decimated wavelet transform) and the Hurst exponent.METHODS:
The signals corresponding to the ten analyzed sequences were obtained by assessing GC content, and then these signals were decomposed using the discrete non-decimated wavelet transform along with the Daubechies wavelet with four null moments at five levels of decomposition. The Hurst exponent was calculated at each decomposition level using five different methods. The cluster analysis was performed using the results obtained for the Hurst exponent.RESULTS:
The aggregated variance, differenced aggregated variance, and aggregated absolute value methods presented the formation of three groups, whereas the Peng and R/S methods presented the formation of two groups. The aggregated variance method exhibited the best results with respect to the group formation between similar strains.CONCLUSION:
The evaluation of Hurst exponent associated with discrete non-decimated wavelet transform can be used as a measure of similarity between genome sequences, thus leading to a refinement in the analysis.
Texto completo:
Disponível
Coleções:
Bases de dados nacionais
/
Brasil
Contexto em Saúde:
ODS3 - Saúde e Bem-Estar
/
Doenças Negligenciadas
Problema de saúde:
Meta 3.8 Atingir a cobertura universal de saúde
/
Doenças Negligenciadas
/
Tuberculose
Base de dados:
LILACS
/
Sec. Est. Saúde SP
/
Coleciona SUS
Assunto principal:
Genoma Bacteriano
/
Análise de Ondaletas
/
Modelos Genéticos
/
Mycobacterium tuberculosis
Limite:
Humanos
Idioma:
Inglês
Revista:
Rev. Soc. Bras. Med. Trop
Ano de publicação:
2020
Tipo de documento:
Artigo
Instituição/País de afiliação:
Empresa Brasileira de Pesquisa Agropecuária/BR
/
Universidade Federal de Lavras/BR