Take a look at the new version of this page: [ beta version ]. Tell us what you think.

ABSTRACT

An automated web based tool for assigning HIV-1 pure and recombinant subtypes within unaligned sequences is presented. The system combines the BLAST search algorithm and the recombination identification program for genetic subtyping of HIV-1. The software was validated through combined analysis of simulated and other HIV-1 real data.

REFERENCES

• 1: Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J.: Basic local alignment search tool. J Mol Biol 215: 403--10.1990
• 2: Araújo, L. V., Soares, M. A., Tanuri, A., Oliveira, S. M., Chequer, P., Sabino, E. C., Ferreira, J. E.: DBCollHIV: A Database System for Collaborative HIV analysis in Brazil. Genetics and molecular research, v. 5, p. 203--215, 2006
• 3: Barreto, C. C., Nishyia, A., Araujo, L. V., Ferreira, J. E., Busch, M. P. and Sabino, E. C.: Trends in antiretroviral drug resistance and clade distributions among HIV-1--infected blood donors in Sao Paulo, Brazil, J Acquir Immune Defic Syndr, 41 (2006) 338--41.
• 4: Durbin, R., Eddy, S., Krogh, A., Mitchison G.: Biological sequence analysis: probabilistic models of proteins and nucleic acids, 1998, Cambridge University Press
• 5: Gifford, R., de Oliveira, T., Rambaut, A., Myers, R. E., Gale, C. V., Dunn, D., Shafer, R., Vandamme, A. M., Kellam, P. and Pillay, D.: Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity, Aids, 20 (2006) 1521--9.
• 6: Gordon, M., De Oliveira, T., Bishop, K., Coovadia, H. M., Madurai, L., Engelbrecht, S., Janse van Rensburg, E., Mosam, A., Smith, A. and Cassol, S.: Molecular characteristics of human immunodeficiency virus type 1 subtype C viruses from KwaZulu-Natal, South Africa: implications for vaccine and antiretroviral control strategies, J Virol, 77 (2003) 2587--99.
• 7: Lole, K. S., Bollinger, R. C., Paranjape, R. S., Gadkari, D., Kulkarni, S. S., Novak, N. G., Ingersoll, R., Sheppard, H. W. and Ray, S. C.: Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination, J Virol, 73 (1999) 152--60.
• 8: Morgado, M. G., Sabino, E. C., Shpaer, E. G., Bongertz, V., Brigido, L., Guimaraes, M. D., Castilho, E. A., Galvao-Castro, B., Mullins, J. I., Hendry, R. M. and et al.: V3 region polymorphisms in HIV-1 from Brazil: prevalence of subtype B strains divergent from North American/European prototype and detection of subtype F, AIDS Res Hum Retroviruses, 10 (1994) 569--76.
• 9: Robertson, D. L., Anderson, J. P., Bradac, J. A., Carr, J. K., Foley, B., Funkhouser, R. K., Gao, F., Hahn, B. H., Kalish, M. L., Kuiken, C., Learn, G. H., Leitner, T., McCutchan, F., Osmanov, S., Peeters, M., Pieniazek, D., Salminen, M., Sharp, P. M., Wolinsky, S. and Korber, B.: HIV-1 nomenclature proposal, Science, 288 (2000) 55--6.
• 10: Sabino, E. C., Shpaer, E. G., Morgado, M. G., Korber, B. T., Diaz, R. S., Bongertz, V., Cavalcante, S., Galvao-Castro, B., Mullins, J. I. and Mayer, A.: Identification of human immunodeficiency virus type 1 envelope genes recombinant between subtypes B and F in two epidemiologically linked individuals from Brazil, J Virol, 68 (1994) 6340--6.
• 11: Salminen, M. O., Carr, J. K., Burke, D. S. and McCutchan, F. E.: Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning, AIDS Res Hum Retroviruses, 11 (1995) 1423--5.
• 12: Sanabani, S., Kleine Neto, W., Kalmar, E. M., Diaz, R. S., Janini, L. M. and Sabino, E. C.: Analysis of the near full length genomes of HIV-1 subtypes B, F and BF recombinant from a cohort of 14 patients in Sao Paulo, Brazil, Infect Genet Evol, 6 (2006) 368--77.
• 13: Sanabani, S., Neto, W. K., de Sa Filho, D. J., Diaz, R. S., Munerato, P., Janini, L. M. and Sabino, E. C.: Full-length genome analysis of human immunodeficiency virus type 1 subtype C in Brazil, AIDS Res Hum Retroviruses, 22 (2006) 171--6.
• 14: Santos, A. F., Sousa, T. M., Soares, E. A., Sanabani, S., Martinez, A. M., Sprinz, E., Silveira, J., Sabino, E. C., Tanuri, A. and Soares, M. A., Characterization of a new circulating recombinant form comprising HIV-1 subtypes C and B in southern Brazil, Aids, 20 (2006) 2011--9.
• 15: Schultz, A. K., Zhang, M., Leitner, T., Kuiken, C., Korber, B., Morgenstern, B. and Stanke, M.: A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes, BMC Bioinformatics, 7 (2006) 265.
• 16: Teixeira, S. L., Bastos, F. I., Telles, P. R., Hacker, M. A., Brigido, L. F., de, F. O. C. A., Bongertz, V. and Morgado, M. G.: HIV-1 infection among injection and ex-injection drug users from Rio de Janeiro, Brazil: prevalence, estimated incidence and genetic diversity, J Clin Virol, 31 (2004) 221--6.

INDEX TERMS

Primary Classification:
  J. Computer Applications
  J.3 LIFE AND MEDICAL SCIENCES

General Terms:
Experimentation, Management

Keywords:
HIV, HIV subtype