Articles
Computational tool for the analysis of HIV mutations associated with susceptibility or resistance to drugs
Published 2009-07-15
Keywords
- Bioinformatics,
- resistance,
- DNA,
- amino acid,
- nucleotiden
- protease,
- reverse transcriptase ...More
How to Cite
Acero Barraza, S. M., Cervantes Acosta, G. J., & Zurek Varela, E. E. (2009). Computational tool for the analysis of HIV mutations associated with susceptibility or resistance to drugs. Revista UIS Ingenierías, 8(1). Retrieved from https://revistas.uis.edu.co/index.php/revistauisingenierias/article/view/239
Abstract
This paper presents the development and implementation of the system that serves as a tool for the study and exploration of Human Immunodefciency Virus (HIV) from computational analysis of these mutations, taking genetic information itself. The analysis is performed using the information contained in the HIV genetic sequence and comparing it to reference sequences. Descriptions of the algorithms for alignment, mutation identifcation and resistance analysis applied to the genetic sequence of the virus are presented.
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References
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L. A. N. Laboratory, “ADRA: Antiviral Drug Resistance Analysis,” Los Alamos National Laboratory, 2007.
S. J. Little and S. Holte, “Antiretroviral-Drug Resistance among Patients Recently Infected with HIV,” The New Englad Journal of Medicine, vol. 347, pp. 385-394, Agosto 8 2002 2002.
E. K. Wagner and M. J. Hewlett., Basic Virology, 2, Illustrated ed.: Blackwell Publishing, 2004.
Mount and W. David, “Bioinformatics: Sequence and Genome Analysis,” New York: Cold Spring Harbor Laboratory Press., 2001.
M. H. Schierupa and J. Hein, “Consequences of Recombination on Traditional Phylogenetic Analysis,” Genetics, vol. 156, pp. 879-891, Octubre 2000 2000.
M. Schena, “DNA Microarrays: A practical Approach,” O. U. Press, Ed., 1999, p. 232.
G. C. Menéndez-Arias, “DR_SEQAN: a PC/ Windows-based software to evaluate drug,” BMC Infectious Diseases, vol. 6, 2006.
H. Tao, “Drug Resistance Mutations Superimposed on the Structures of HIV-1 Proteaseand Reverse Transcriptase,” in HIV Molecular Immunology Database New Mexico: Theoretical Biology and Biophysics Group, 1997.
D. L. Hartl, Essential Genetics: A Genomics Perspective, 3 ed.: Jones and Bartlett Publishers, 1995, 1995.
B. N. Fields, D. M. Knipe, P. M. Howley, and D. E. Griffn, Fields’ virology, 5 ed.: Lippincott Williams & Wilkins, 2006.
S. B. Needleman and C. D. Wunsch, “A general method Applicable to the search for similarities in the aminoacid sequence or twon proteins,” J. Mol. Biol., vol. 48, pp. 443-453, 1970.
N. Beerenwinkel, T. Lengauer, J. Selbig, B. Schmidt, H. Walte, K. Korn, R. Kaiser, and D. Hoffmann., “Geno2pheno: interpreting genotypic HIV drug resistance tests,” Intelligent Systems, IEEE, vol. 16, pp. 35-41, nov - dic 2001 2001.
C. Pasquier, N. Millot, R. Njouom, K. Sandres, M. Cazabat, J. Puel, and J. Izopet, “HIV-1 subtyping using phylogenetic analysis of pol gene sequences,” Journal of vyrological Methods, vol. 92, pp. 45-54,
Abril 30 2001 2001.
M. S. Hirsch, “HIV Drug Resistance - A Chink in the Armor,” The New Englad Journal of Medicine, vol. 347, pp. 438-439, Agosto 8 2002 2002.
C. Yabar, P. Chavez, Z. Varas, and R. Rodriguez, “Identifcación molecular de mutaciones puntuales relacionadas con resistencia a drogas en VIH-1 de pacientes peruanos,” Revista Peruana de Medicina experimental y Salud Publica, vol. 23, pp. 149-157, Julio - Septiembre 2006 2006.
N. J. Dimmock, A. Easton, and K. Leppard, Introduction to Modern Virology, 5, Illustrated ed.: Blackwell Publishing, 2001.
R. G. Cotton, E. Edkins, and S. Forrest, “Mutation Detection: A practical Approach,” Oxford University Press, 1999, p. 264.
S. Clark, C. Calef, and J. Mellors, “Mutations in Retroviral Genes Associated with Drug Resistance “ in HIV Sequence Compendium 2006/200, F. B. Thomas Leitner T, Hahn B, Marx P, McCutchan F, Mellors J, Wolinsky S, Korber B., Ed.: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM. LA-UR 07- 4826, 2007, pp. 58-158.
W. M. Fitch and T. F. Smith, “Optimal Sequence Alignments,” Procedings of the National Academy of Sciences of the United States of America, vol. 80, pp. 1382-1386, 1983.
M. M. Miyamoto and J. Cracraft, “Phylogenetic Analysis of DNA Sequences,” New York: Oxford University Press, Incorporated, 1991, p. 369.
D. Costagliola, L. Assoumou, and L. MorandJoubert, “Prevalence of HIV-1 drug resistance in treated patients - A French nationwide study,” JAIDSJournal Of Acquired Immune Defciency Syndromes, vol. 46, pp. 12-18, septiembre 1 2007 2007.
J. M. Coffn, S. H. Hughes, and H. E. Varmus, Retroviruses, illustrated ed.: CSHL Press, 1997.
Y. Xing, “Sequence Alignment Algorithm,” in School of electronics Engineering and Computer Science Beijing: Peking University, 2005.
A. Abecasis, A. Vandamme, and P. Lemey, “Sequence Alignment in HIV Computational Analysis “ in HIV Sequence Compendium 2006/2007: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM. LA-UR 07-4826, 2007.
S.Yerly, L. Kaiser, E. Race, J. Bru, F. Clavel, and LPerrin, “Transmision of antirretroviral drug-resistant HIV-1 variants,” Lancet, vol. 354, p. 729, 1999.
V. A. Johnson and F. Brun-Vézinet, “Update of the drug Resistance Mutations in HIV-1,” Topics in HIV Medicine, vol. 16, pp. 62-68, 2008.
W. E. Highsmith, Q. Jin, A. J. Nataraj, J. M. O’Connor, V. D. Burland, W. R. Baubonis, F. P. Curtis, N. Kusukawa, and M. M. Garner, “Use of a DNA toolbox for the characterization of mutation scanning methods. I: Construction of the toolbox and evaluation of heteroduplex analysis,” Electropheresis, vol. 20, pp. 1186-1194, Mayo 26 1999 1999.
V. G. S. Merino, “Variacion de los genes accesorios y su implicacion en la biología del vih-1,” in Departamento de microbiología II. vol. Doctor Madrid: Universidad Complutense de Madrid, 2001, p. 700.