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. 2020 Nov:96:106683.
doi: 10.1016/j.asoc.2020.106683. Epub 2020 Sep 3.

Analyzing COVID-19 virus based on enhanced fragmented biological Local Aligner using improved Ions Motion Optimization algorithm

Mohamed Issa  1 , Mohamed Abd Elaziz  2   3
Affiliations

Analyzing COVID-19 virus based on enhanced fragmented biological Local Aligner using improved Ions Motion Optimization algorithm

Mohamed Issa et al. Appl Soft Comput. 2020 Nov.

Abstract

SARS-CoV-2 (COVID-19) virus is a havoc pandemic that infects millions of people over the world and thousands of infected cases dead. So, it is vital to propose new intelligent data analysis tools and enhance the existed ones to aid scientists in analyzing the COVID-19 virus. Fragmented Local Aligner Technique (FLAT) is a data analysis tool that is used for detecting the longest common consecutive subsequence (LCCS) between a pair of biological data sequences. FLAT is an aligner tool that can be used to find the LCCS between COVID-19 virus and other viruses to help in other biochemistry and biological operations. In this study, the enhancement of FLAT based on modified Ions Motion Optimization (IMO) is developed to produce acceptable LCCS with efficient performance in a reasonable time. The proposed method was tested to find the LCCS between Orflab poly-protein and surface glycoprotein of COVID-19 and other viruses. The experimental results demonstrate that the proposed model succeeded in producing the best LCCS against other algorithms using real LCCS measured by the SW algorithm as a reference.

Keywords: COVID-19 virus; Ions motion optimization; Longest common consecutive substrings; Pairwise local alignment; Smith–Waterman alignment algorithm.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
Synergy of exploration and exploitation over the sequence length for FLAT.
Fig. 2
Fig. 2
A representation of the fragmentation of sequences into short fragments.
Fig. 3
Fig. 3
A framework explaining the rule of using FLAT and the relation with other applications on COVID-19.
Fig. 4
Fig. 4
Description of FLAT based on the improved IMO algorithm for aligning COVID-19 with other viruses.
Fig. 5
Fig. 5
Measuring of length of LCCS relative to the maximum length of the pair of sequences.
Fig. 6
Fig. 6
Comparison of time performance of the SW algorithm and FLAT based on improved optimization algorithms.
None
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See this image and copyright information in PMC

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