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Reseach Article
Analysis of Philogenetic SARS-CoV-2 on BLAST Query using Recursive Similarity Search
| International Journal of Computer Applications |
| Foundation of Computer Science (FCS), NY, USA |
| Volume 186 - Number 27 |
| Year of Publication: 2024 |
| Authors: Rodiah, Diana Tri Susetianingtias, Eka Patriya |
10.5120/ijca2024923754
|
Rodiah, Diana Tri Susetianingtias, Eka Patriya . Analysis of Philogenetic SARS-CoV-2 on BLAST Query using Recursive Similarity Search. International Journal of Computer Applications. 186, 27 ( Jul 2024), 13-19. DOI=10.5120/ijca2024923754
Abstract
One method for examining the presence of mutations in the genetic diversity of SARS-CoV involves conducting a phylogenetic tree analysis. To construct a phylogenetic tree, it is necessary to obtain suitable RNA samples. This is achieved by comparing user queries to search for sequence similarity in the NCBI database using the BLAST algorithm. It is necessary to narrow down the sample by selecting data prior to constructing a phylogenetic tree using the BLAST Query. The purpose of this action is to streamline the process of interpreting the outcomes derived from the construction of a phylogenetic tree. This study presents a novel approach for enhancing the efficiency of the BLAST Query through the utilization of four recursive searches. The optimization of BLAST queries involves selecting taxa from the experimental phylogenetic tree that exhibit sufficient dissimilarity from the input taxa. These selected taxa are then utilized as query inputs in subsequent search optimizations. Additionally, the length of the query is specifically reduced in the ORF1ab gene region. The phylogenetic tree derived from the four experiments yielded divergent interpretations, particularly in the second experiment where the taxa exhibited a high degree of homology. The optimization technique employed for BLAST queries enables the reduction of taxa samples that are to be represented in the phylogenetic tree. The present study holds the potential to serve as a valuable resource for identifying samples and constructing a phylogenetic tree for SARS-CoV-2. This, in turn, can facilitate further genetic investigations pertaining to potential viral developments, including the examination of viral mutations.
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