A web-based genotyping resource for viral sequences
National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Building 38A, Room S602, 8600 Rockville Pike, Bethesda, MD 20892, USA, 1 Novartis Institutes for BioMedical Research, Novartis Pharma AG, 4002 Basel, Switzerland and 2 ViroLogic, Inc., South San Francisco, CA 94080, USA
* To whom correspondence should be addressed. Tel: +1 301 435 5756; Fax: +1 301 480 2918; Email: tatiana{at}ncbi.nlm.nih.gov
Received February 20, 2004; Revised and Accepted April 5, 2004
The Genotyping tool at the National Center for Biotechnology Information is a web-based program that identifies the genotype (or subtype) of recombinant or non-recombinant viral nucleotide sequences. It works by using BLAST to compare a query sequence to a set of reference sequences for known genotypes. Predefined reference genotypes exist for three major viral pathogens: human immunodeficiency virus 1 (HIV-1), hepatitis C virus (HCV) and hepatitis B virus (HBV). User-defined reference sequences can be used at the same time. The query sequence is broken into segments for comparison to the reference so that the mosaic organization of recombinant sequences could be revealed. The results are displayed graphically using color-coded genotypes. Therefore, the genotype(s) of any portion of the query can quickly be determined. The Genotyping tool can be found at: http://www.ncbi.nih.gov/projects/genotyping/formpage.cgi.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  X. Wu, Z. Cai, X.-F. Wan, T. Hoang, R. Goebel, and G. Lin Nucleotide composition string selection in HIV-1 subtyping using whole genomes Bioinformatics, July 15, 2007; 23(14): 1744 - 1752. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 O. Lada, Y. Benhamou, T. Poynard, and V. Thibault Coexistence of Hepatitis B Surface Antigen (HBs Ag) and Anti-HBs Antibodies in Chronic Hepatitis B Virus Carriers: Influence of "a" Determinant Variants J. Virol., March 15, 2006; 80(6): 2968 - 2975. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Laperche, K. Saune, P. Deny, G. Duverlie, S. Alain, M.-L. Chaix, C. Gaudy, F. Lunel, J.-M. Pawlotsky, C. Payan, et al. Unique NS5b Hepatitis C Virus Gene Sequence Consensus Database Is Essential for Standardization of Genotype Determinations in Multicenter Epidemiological Studies J. Clin. Microbiol., February 1, 2006; 44(2): 614 - 616. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. de Oliveira, K. Deforche, S. Cassol, M. Salminen, D. Paraskevis, C. Seebregts, J. Snoeck, E. J. van Rensburg, A. M. J. Wensing, D. A. van de Vijver, et al. An automated genotyping system for analysis of HIV-1 and other microbial sequences Bioinformatics, October 1, 2005; 21(19): 3797 - 3800. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. E. Myers, C. V. Gale, A. Harrison, Y. Takeuchi, and P. Kellam A statistical model for HIV-1 sequence classification using the subtype analyser (STAR) Bioinformatics, September 1, 2005; 21(17): 3535 - 3540. [Abstract] [Full Text] [PDF]
|
|