Journal: IPSI Transactions on Internet Research

Surface Glycoprotein Classification
Using Repeat Sequences

Authors: Alshafah, Samira A. Beljanski, Miloš V. and Mitić, Nenad S.


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Abstract

Correct recognition of sequence characteristics is one of the most important steps in bioinformatics. The paper presents a method for the characterization of surface glycoprotein in different viruses. The method uses amino-acid and nucleotide repeat sequences to form a virus/protein profile that is used to characterize and predict the type of protein. Based on a set of characteristic repetitive sequences, a classification model for predicting the type of virus was constructed.


Keywords

classification, coronavirus, filoviridae, repeat sequences, surface glycoprotein


Published in: IPSI Transaction on Internet Research (Volume: 21, Issue: 2)
Publisher: IPSI, Belgrade

Date of Publication: July 1, 2025

Open Access: CC-BY-NC-ND
DOI: 10.58245/ipsi.tir.2502.10

Pages: 100 - 106

ISSN: 1820 - 4503

References

1. Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, Graham BS, McLellan JS. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science. 2020 Mar 13;367(6483):1260- 1263. doi: 10.1126/science.abb2507. Epub 2020 Feb 19. PMID: 32075877; PMCID: PMC7164637

2. Jain S, Martynova E, Rizvanov A, Khaiboullina S, Baranwal M.: Structural and Functional Aspects of Ebola Virus Proteins. Pathogens. 2021 Oct15;10(10):1330. doi: 10.3390/pathogens10101330. PMID: 34684279; PMCID: PMC8538763.

3. Huang, Y., Yang, C., Xu, Xf. et al. Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19. Acta Pharmacol Sin 41, 1141–1149 (2020). https://doi.org/10.1038/s41401-020-0485-4

4. Kyriakidis NC, López-Cortés A, González EV, Grimaldos AB, Prado EO. SARS-CoV-2 vaccines strategies: a comprehensive review of phase 3 candidates. NPJ Vaccines. 2021 Feb 22;6(1):28. doi: 10.1038/s41541-021-00292-w. PMID: 33619260; PMCID: PMC7900244

5. Holmudden M, Gustafsson J, Bertrand YJK, Schliep A, Norberg P. Evolution shapes and conserves genomic signatures in viruses. Commun Biol. 2024 Oct 30;7(1):1412. doi: 10.1038/s42003-024-07098-1. PMID: 39478059; PMCID: PMC11526014.

6. Luo H, Nijveen H. Understanding and identifying amino acid repeats. Brief Bioinform. 2014 Jul;15(4):582-91. doi: 10.1093/bib/bbt003. PMID: 23418055; PMCID: PMC4103538.

7. Jelovic A, Mitic N, Eshafah S, Beljanski M. Finding Statistically Significant Repeats in Nucleic Acids and Proteins. J Comput Biol. 2018 Apr;25(4):375-387. doi: 10.1089/cmb.2017.0046.

8. Tan, P-N, Steinbach, M., Karpatne, A., Kumar, V. Introduction to Data Mining (2nd Edition), ISBN 0133128903, Pearson, 2018

9. Silva JM, Pratas D, Caetano T, Matos S. The complexity landscape of viral genomes. Gigascience. 2022 Aug 11;11:giac079. doi: 10.1093/gigascience/giac079. PMID: 35950839; PMCID: PMC9366995.

10. Jelović A.: RepeatsPlus - program for finding motifs and repeats in data sequences, J. Bioinf. Comput. Biol., 19 (3), p. 2150010, doi: 10.1142/S0219720021500104, 2021

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Samira A. Alshafah

Samira Al-Shafah is an assistant professor in the Department of Computer Science at the Faculty of Education, Az-Zawiya University. She obtained her Master's degree in 2007 in Computer Science from the Academy of Graduate Studies and her PhD in Computer Science, specializing in Information Technology, from the Faculty of Computer Science and Mathematics, University of Belgrade, Serbia. Her research interests focus on bioinformatics and data mining.
Email: Samira_7_8@yahoo.com

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Beljanski Miloš V.

Miloš Beljanski is a Molecular Biologist and Principal research fellow, retired from the Institute of General and Physical Chemistry/Biolab, Belgrade. He received his BSc, MSc and DrSci from the University of Belgrade, Faculty of Sciences, Dept. of Biology. His research interests cover areas of Biophysical Chemistry and Bioinformatics.
Email: mbel@matf.bg.ac.rs

× Mitić Nenad S.

Nenad Mitić is a full Professor at the Department of Computer Science, Faculty of Mathematics, University of Belgrade. He received his BSc, MSc and PhD from the University of Belgrade, Faculty of Mathematics. From 1983 to 1991 he was a system analyst on an IBM mainframe in the Statistical Office of the Republic of Serbia, Belgrade. From 1991 till now he has been with the Faculty of Mathematics, Belgrade. His research interests cover areas of bioinformatics, data mining, big data and functional programming. Currently, he is the president of the Serbian Society for Bioinformatics and Computational Biology.
Email: nenad.mitic@matf.bg.ac.rs, ORCID 0000-0002-0556-6279

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Cite this article

Alshafah, Samira A.; Beljanski, Miloš V.; and Mitić, Nenad S.
"Surface Glycoprotein Classification Using Repeat Sequences",
IPSI Transactions on Internet Research, vol. 20(2), pp. 100-106, 2025. https://doi.org/10.58245/ipsi.tir.2502.10