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Nucleic Acids Research 2004 32(Web Server Issue):W654-W659; doi:10.1093/nar/gkh419
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

A web-based genotyping resource for viral sequences

Mikhail Rozanov, Uwe Plikat1, Colombe Chappey2, Andrey Kochergin and Tatiana Tatusova*

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.


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