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Mathematical Modeling and Classification of Viruses from Herpesvirus Family

by Gaber H. Alsayed, Ahmed M. Alzohairy, Rania. B. M. Amer, Mohammed M. Saleh, Osama M. Abdo
journal cover thumbnail

International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 87 - Number 12
Year of Publication: 2014
Authors: Gaber H. Alsayed, Ahmed M. Alzohairy, Rania. B. M. Amer, Mohammed M. Saleh, Osama M. Abdo
10.5120/15258-3696

Gaber H. Alsayed, Ahmed M. Alzohairy, Rania. B. M. Amer, Mohammed M. Saleh, Osama M. Abdo . Mathematical Modeling and Classification of Viruses from Herpesvirus Family. International Journal of Computer Applications. 87, 12 ( February 2014), 5-13. DOI=10.5120/15258-3696

@article{ 10.5120/15258-3696,
author = { Gaber H. Alsayed, Ahmed M. Alzohairy, Rania. B. M. Amer, Mohammed M. Saleh, Osama M. Abdo },
title = { Mathematical Modeling and Classification of Viruses from Herpesvirus Family },
journal = { International Journal of Computer Applications },
issue_date = { February 2014 },
volume = { 87 },
number = { 12 },
month = { February },
year = { 2014 },
issn = { 0975-8887 },
pages = { 5-13 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume87/number12/15258-3696/ },
doi = { 10.5120/15258-3696 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T22:05:42.728053+05:30
%A Gaber H. Alsayed
%A Ahmed M. Alzohairy
%A Rania. B. M. Amer
%A Mohammed M. Saleh
%A Osama M. Abdo
%T Mathematical Modeling and Classification of Viruses from Herpesvirus Family
%J International Journal of Computer Applications
%@ 0975-8887
%V 87
%N 12
%P 5-13
%D 2014
%I Foundation of Computer Science (FCS), NY, USA
Abstract

The process of modeling and classifications of viruses that belong to a specific family is an important for biologist and for many biological applications. There are many ways for Viruses families' classification. The degree of similarity or diversity among the structure of the viruses capsid proteins is very useful in studying the Viruses families' classification and their genetic evolution . It also important propose if we construct a mathematical model of the virus life cycle to be able to fully understand the life cycle of Viruses families' activities . In this paper we introduce a proposed mathematical model for some Herpesvirus family viruses simple life cycle and comprehensive study for its classification using sequence alignment algorithms in order to demonstrate their genetic evolution according to the structure of their capsid protein. Herpesvirus family is considered one of the most important family in the families of the enveloped DNA viruses as it contain many dangerous viruses for human health. This family contain one of newly discovered viruses called Epstein–Barr virus (EBV), also called human herpesvirus 4 (HHV-4), which is one of the most common viruses in human. Infection with EBV occurs by the oral transfer of saliva [1] and genital secretions.

References
  1. Amon, Wolfgang; Farrell (November 2004). "Reactivation of Epstein–Barr virus from latency". Reviews in Medical Virology 15 (3): 149–56. doi:10. 1002/rmv. 456. PMID 15546128. Retrieved 28 May 2012.
  2. Volk et al, "essential of medical microbiology" 4th edition 1991.
  3. Richard A. Harvey, Pamela C. Champe, Bruce D. Fisher "Lippincott's microbiology 2th Edittion" Section 4 Chapter 25, (2007).
  4. Ryan KJ; Ray CG (editors) "Sherris Medical Microbiology (4th ed. ) ". McGraw Hill. ISBN 0-8385-8529-9. (2004).
  5. Mettenleiter et al. "Molecular Biology of Animal Herpesviruses". Animal Viruses: Molecular Biology. Caister Academic Press. ISBN 1-904455-22-0. . (2008). [http://www. horizonpress. com/avir].
  6. Sandri-Goldin RM (editor). " Alpha Herpesviruses: Molecular and Cellular Biology". Caister Academic Press. ISBN 978-1-904455-09-7. (2006).
  7. .
  8. Chayavichitsilp P, Buckwalter JV, Krakowski AC, Friedlander SF. "Herpes simplex". Pediatr Rev 30 (4): 119–29; quiz 130. doi:10. 1542/pir. 30-4-119. PMID 19339385. April 2009.
  9. In the United States, as many as 95% of adults between 35 and 40 years of age have been infected. National Center for Infectious Diseases
  10. Staras SA, Dollard SC, Radford KW, Flanders WD, Pass RF, Cannon MJ (November 2006). "Seroprevalence of cytomegalovirus infection in the United States, 1988–1994". Clin. Infect. Dis. 43 (9): 1143–51. doi:10. 1086/508173. PMID 17029132. Retrieved 2009-12-04.
  11. Jay C. Brown, William W. Newcomb. "Herpesvirus Capsid Assembly: Insights from Structural Analysis". Current Opinion in Virology 1 (2): 142–149. 2011 August 1.
  12. John Carter, Venetia Saunders. "Virology, Principles and Applications". John Wiley & Sons. ISBN 978-0-470-02386-0.
  13. Madigan M, Martinko J (2006). Brock Biology of Microorganisms (11th ed. ). Prentice Hall. ISBN 0-13-144329-1.
  14. N. Komarova, D. Wodarz, ODE models for oncolytic virus dynamics, J of Theoretical Biology, 263(2010) 530-543.
  15. Y Wang, JP Tian, J Wei. Lytic cycle: A defining process in oncolytic virotherapy. Applied Mathematical Modelling, Vol. 37, Issue 8, 15 April 2013, Pages 5962–5978?
  16. C. S. B Needleman, C. D. Wunsch, "A general method applicable to the search for similarities in the amino acid sequence of two proteins". Journal of molecular biology, vol. 48, no. 1, pp. 443-453. 1970.
  17. Mohammed M. Saleh, Ahmed M. Alzohairy, Osama Abdo Mohamed, Gaber H. Alsayed (2013). A Comprehensive Study by Using Different Alignment Algorithms to Demonstrate the Genetic Evolution of Heat Shock Factor 1 (HSF1) in Different Eukaryotic Organisms. IRACST – Engineering Science and Technology: An International Journal (ESTIJ), ISSN: 2250-3498, Vol. 3, No. 2 Pages:376-382.
  18. Mansour A, Jaime A. Teixeira da Silva, Gábor Gyulai (2009) Assessment of molecular (dis) similarity: The role of multiple sequence alignments (MSA) programs in biological research. Genes, genomes and genomics. 3 (Special Issue 1): 23-30 (Print ISSN 1749-0383) (Bioinformatics SI).
  19. Mohamed Issa, Hitham Abo Bakr, Ahmed M. Alzohairy and Ibrahim Zeidan (2012) Gene-Tracer: Algorithm Tracing Genes Modification from Ancestors through Offsprings. in International Journal of Computer Applications (IJCA) 52(19):11-14
  20. X. Huang, K. M. Chao, "A generalized global alignment algorithm, Bioinformatics", Vol. 19, N°2: (2003), p228–233.
  21. R. A. Cartwright: Ngila, "global pairwise alignments with logarithmic and affine gap costs", Bioinformatics, Vol. 23, N°11:, p1427–1428. (2007).
  22. T. F. Smith, M. S. Waterman, "Identification of common molecular subsequences", J. Molecular Biology, no. 147, pp. 195-197, 1981.
  23. Thompson J. D. , Higgins D. G. , Gibson T. J. , CLUSTAL W" improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice" Nucleic Acids Res, vol. 22. pp. 4673–4680, (1994).
  24. M. O. Dayhoff, R. M. Schwartz, B. C. Orcutt, "A model of evolutionary change in proteins, in Atlas of Protein Sequence and Structure", chapter 22, National Biomedical Research Foundation, Washington, DC: (1978), p345–358.
  25. S. Henikoff, J. G. Henikoff, "Amino acid substitution matrices from protein blocks", Proc. Natl. Acad. Sci. USA, Vol. 89, N°22: (1992), p10915-10919.
  26. Alzohairy, A. Mansour, Margaret H. MacDonald, Benjamin F. Matthews (2013). The pJan25 vector series: An enhancement of the gateway-compatible vector pGWB533 for broader promoter testing applications. Plasmid (2013), 69(3):249-56
  27. Alzohairy, A. Mansour. Gábor Gyulai, Jansen RK. A. Bahieldin (2013) Transposable Elements Domesticated and neofunctionalized by Eukaryotic Genomes PLASMID. 69 (2013) 1–15.
  28. Mansour, A. (2008). Utilization of Genomic Retrotransposon as cladistic molecular markers. Journal of Cell and Molecular Biology. 7(1): 17-28.
  29. Mansour, A. Epigenetic activation of Genomic Retrotransposon (2007). Journal of Cell and Molecular Biology. 6 (2): 99-107
  30. Mansour A. (2009). Water Deficit Induction of Copia and Gypsy Genomic Retrotransposons. Plant Stress 3(1)33-39
  31. Alzohairy, A. Mansour , Mohamed A Yousef, Sherif S Edris, Balázs Kerti and Gábor Gyulai (2012). Detection of long terminal repeat (LTR) retrotransposons reactivation induced by in vitro environmental stresses in barley (Hordeum vulgare) via reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Life Science Journal (2012; 9(4): 5019-5026.
  32. Ahmed Alzohairy, J. S. M. Sabir, Gabor Gyulai, Rania Younis, Robert Jansen, Ahmed Bahieldin (2014) Environmental Stress Activation of Plant LTR-Retrotransposons. Functional Plant Biology. (In press 2014)
Index Terms

Computer Science
Information Sciences

Keywords

Pairwise global alignment multiple sequence alignment dot plot matrix herpesvirus family phylogenetic tree MatLab Phylogenetic.

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