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

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.

[1]  Vikram Kumar Kamboj.  A novel hybrid PSO–GWO approach for unit commitment problem , 2015, Neural Computing and Applications.

[2]  J. Epstein,et al.  Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor , 2013, Nature.

[3]  Xiao-Feng Xie,et al.  DEPSO: hybrid particle swarm with differential evolution operator , 2003, SMC'03 Conference Proceedings. 2003 IEEE International Conference on Systems, Man and Cybernetics. Conference Theme - System Security and Assurance (Cat. No.03CH37483).

[4]  Stergios B. Fotopoulos,et al.  Introduction to Modern Nonparametric Statistics , 2004, Technometrics.

[5]  L. Chuang,et al.  Breast Cancer Risk Prediction Using Ions Motion Optimization Algorithm , 2016 .

[6]  Trong-The Nguyen,et al.  Hybrid Particle Swarm Optimization with Bat Algorithm , 2014, ICGEC.

[7]  Ajoy Kumar Chakraborty,et al.  Quasi-reflected ions motion optimization algorithm for short-term hydrothermal scheduling , 2018, Neural Computing and Applications.

[9]  Jianping Hu,et al.  COVID-19 Docking Server: A meta server for docking small molecules, peptides and antibodies against potential targets of COVID-19 , 2020, Bioinform..

[10]  David H. Wolpert,et al.  No free lunch theorems for optimization , 1997, IEEE Trans. Evol. Comput..

[11]  Trong-The Nguyen,et al.  Diversity Enhanced Ion Motion Optimization for Localization in Wireless Sensor Network , 2019, J. Inf. Hiding Multim. Signal Process..

[12]  Jamal Abd Ali,et al.  Optimization techniques to enhance the performance of induction motor drives: A review , 2018 .

[13]  Seyed Mohammad Mirjalili,et al.  Ions motion algorithm for solving optimization problems , 2015, Appl. Soft Comput..

[14]  Qianyun Liu,et al.  Emerging coronaviruses: Genome structure, replication, and pathogenesis , 2020, Journal of medical virology.

[15]  Alex Alves Freitas,et al.  A hybrid particle swarm/ant colony algorithm for the classification of hierarchical biological data , 2005, Proceedings 2005 IEEE Swarm Intelligence Symposium, 2005. SIS 2005..

[16]  Sami Khuri,et al.  A Comparison of DNA Fragment Assembly Algorithms , 2004, METMBS.

[17]  A Harrag,et al.  Three-diodes PV model parameters extraction using PSO algorithm , 2019 .

[18]  R F Doolittle,et al.  Progressive alignment and phylogenetic tree construction of protein sequences. , 1990, Methods in enzymology.

[19]  T. Bakhshpoori,et al.  An efficient hybrid Particle Swarm and Swallow Swarm Optimization algorithm , 2014 .

[20]  H. Burman.  Principles of General Chemistry , 1968 .

[21]  J. Garnier,et al.  Improving protein secondary structure prediction with aligned homologous sequences , 1996, Protein science : a publication of the Protein Society.

[22]  D. Spandidos,et al.  A dissection of SARS-CoV2 with clinical implications (Review) , 2020, International journal of molecular medicine.

[23]  M. E. Hassan,et al.  Cloud Job ‎Scheduling with‎ Ions Motion Optimization Algorithm , 2020 .

[24]  Parth Sarthi Sen Gupta,et al.  Binding insight of clinically oriented drug famotidine with the identified potential target of SARS-CoV-2 , 2020, Journal of biomolecular structure & dynamics.

[25]  Vandana,et al.  Estimation of Photovoltaic Cells Model Parameters using Particle Swarm Optimization , 2014 .

[26]  Ali Dabbagh,et al.  The role of artificial intelligence in management of critical COVID-19 patients , 2020 .

[27]  Zhicheng Ji,et al.  A novel hybrid particle swarm optimization and gravitational search algorithm for solving economic emission load dispatch problems with various practical constraints , 2014 .

[28]  Jacques Cohen,et al.  Bioinformatics—an introduction for computer scientists , 2004, CSUR.

[29]  Yuanyang Zou,et al.  The whirlpool algorithm based on physical phenomenon for solving optimization problems , 2019, Engineering Computations.

[30]  Aboul Ella Hassanien,et al.  ASCA-PSO: Adaptive sine cosine optimization algorithm integrated with particle swarm for pairwise local sequence alignment , 2018, Expert Syst. Appl..

[31]  Behrooz Vahidi,et al.  A novel physical based meta-heuristic optimization method known as Lightning Attachment Procedure Optimization , 2017, Appl. Soft Comput..

[32]  Vijander Singh,et al.  A novel nature-inspired algorithm for optimization: Squirrel search algorithm , 2019, Swarm Evol. Comput..

[33]  Hussain Shareef,et al.  Lightning search algorithm , 2015, Appl. Soft Comput..

[34]  Mir Saman Pishvaee,et al.  Electron radar search algorithm: a novel developed meta-heuristic algorithm , 2020, Soft Comput..

[35]  Seyedali Mirjalili,et al.  SCA: A Sine Cosine Algorithm for solving optimization problems , 2016, Knowl. Based Syst..

[36]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[37]  Ehab Saliem Ali Mohamed Salamh.  A Hybrid Particle Swarm Optimization and Bacterial Foraging for Optimal Power System Stabilizers Design , 2013 .

[38]  Manoj Kumar Debnath,et al.  IMO-based novel adaptive dual-mode controller design for AGC investigation in different types of systems , 2020 .

[39]  R. Gandhi.  Clinical Characteristics of 2019 Novel Coronavirus Infection , 2020 .

[40]  Li-Yeh Chuang,et al.  Protein folding prediction in the HP model using ions motion optimization with a greedy algorithm , 2018, BioData Mining.

[41]  Zhijiang Du,et al.  A universal index and an improved PSO algorithm for optimal pose selection in kinematic calibration of a novel surgical robot , 2018 .

[42]  Wei Kong,et al.  Hybrid particle swarm optimization and tabu search approach for selecting genes for tumor classification using gene expression data , 2008, Comput. Biol. Chem..

[43]  Riccardo Poli,et al.  Particle swarm optimization , 1995, Swarm Intelligence.

[44]  Harish Garg,et al.  A hybrid PSO-GA algorithm for constrained optimization problems , 2016, Appl. Math. Comput..

[45]  Reza Moghdani,et al.  Volleyball Premier League Algorithm , 2018, Appl. Soft Comput..

[46]  W. Liang,et al.  Clinical characteristics of 2019 novel coronavirus infection in China , 2020, medRxiv.

[47]  Trong-The Nguyen,et al.  A Multi-objective Ions Motion Optimization for Robot Path Planning , 2018, Advances in Engineering Research and Application.

[48]  S Cauchemez,et al.  Transmission scenarios for Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and how to tell them apart. , 2013, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.