Profiling DNA Sequence of SARS-Cov-2 Virus Using Machine Learning Algorithm

Abstract

Corona virus disease-19 (COVID-19) is growing rapidly because it is an infectious disease. This disease is caused by a virus belonging to the type of DNA virus with very diverse genetics. This study proposes a feature extraction method using k-mer to obtain nucleotide frequencies in protein coding. In profiling viral DNA sequences, this study proposes to obtain similarity by country using hierarchical k-means, where the results are averaged by the hierarchical clustering method and then find the initial cluster center. The experimental results show that the silhouette, purity, and entropy are 0.867, 0.208, and 0.892, respectively. Then, we apply the Gini index feature selection to find the important components as characteristics in each country. The selected components are implemented using the ensemble method, Random Forest, to evaluate their performance. The experimental results showed high performance, including sensitivity, accuracy, specificity, and area under the curve (AUC).

Country-Based COVID-19 DNA Sequence Classification in Relation with International Travel Policy

“…Several strains that were isolated before the national implementation of border control exhibited a high degree of invariance, while others demonstrated approximately 80% of synonymous mutations, suggesting possible ongoing virus adaptation in the region [23]. Focused on DNA, research related to sequence profiling has been carried out regionally, involving five ASEAN countries with a relatively limited number of sequences [24]. To enhance the analysis with a larger dataset and provide clear information on how the virus' DNA differs between countries, particularly where the countries are geographically close to each other, this paper purposes to classify SARS-CoV-2 DNA sequences based on the country using a deep learning model.…”

DMAV: Enhanced MAV Link Protocol Using Dynamic DNA Coding for Unmanned Aerial Vehicles

“…For this reason, unmanned aerial vehicles are at risk of being compromised [17]. One of the most exciting areas in the world of information technology is the field of DNA cryptography [18]. DNA cryptography is a method that uses DNA as an information carrier to protect sensitive information.…”