Implementation of Hierarchical Clustering Method in Analyzing Genetic Relationship on DNA SARS-CoV-2 Sequences

Banjarnahor, Evander; Bustamam, Alhadi; Mangunwardoyo, Wibowo; Sarwinda, Devvi

doi:10.1088/1742-6596/1811/1/012074

Cited by 2 publications

(2 citation statements)

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“…where index i loops all the values in the vector. The Euclidean matrix distance is a measure of the geometric distance between two components based on the size (Matthiesen in [22]). The Euclidean distance is used to calculate each distance from each sequence after the 18dimensional MEV data is found.…”

Section: Distance Matrixmentioning

confidence: 99%

“…The results of this study showed accurate and similar results when compared to other alignment methods using ClustalW, Clustal, MAFFT, and MUSCLE. A study by Banjarnahor et al [22] used hierarchical clustering and multiple sequence alignment (MSA) to analyze the SARS-CoV-2 DNA sequence. According to the findings of this study, the ancestors of SARS-CoV-2 originated in China.…”

Section: Introductionmentioning

confidence: 99%

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Analysing Kinship in Severe Acute Respiratory Syndrome Coronavirus 2 DNA Sequences Based on Hierarchical and K-Means Clustering Methods Using Multiple Encoding Vector

Banjarnahor¹,

Bustamam²,

Siswantining³

et al. 2022

Int. J. Adv. Sci. Eng. Inf. Technol.

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Based on the World Health Organization data obtained in mid-April 2021, Coronavirus or Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has already infected more than 134.9 million people worldwide. The virus attacks human breathing, which can cause lung infections and even death. More than 2.9 million people worldwide have died due to coronavirus infection. Meanwhile, more than 1.5 million people in Indonesia have been infected, and 42.5 thousand died because of this coronavirus. Based on this data, carrying out a kinship analysis of the coronavirus is important to reduce its spread. Identifying the kinship of the COVID-19 virus and its spread can be done by forming a phylogenetic tree and clustering. This study uses the Multiple Encoding Vector method in analyzing the sequences and Euclidean distance to determine the distance matrix. This research will then use the Hierarchical clustering method to determine the number of initial centroids, which will be used later by the K-Means clustering method kinship in the SARS-CoV-2 DNA sequence. This study took samples of DNA sequences of SARS-CoV-2 from several infected countries. From the simulation results, the ancestors of SARS-CoV-2 came from China. The analysis results also show that the closest ancestors of COVID-19 to Indonesia came from India. The SARS-CoV-2 DNA sequence also consisted of nine clusters, and the sixth cluster has the greatest number of members.

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Section: Distance Matrixmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%