A web-based genotyping resource for viral sequences

Nucleic Acids Research

Volumn 32, Issue WEB SERVER ISS., 2004, Pages

  Rozanov, Mikhail ^c   Plikat, Uwe ^a   Chappey, Colombe ^b   Kochergin, Andrey ^c   Tatusova, Tatiana ^c  

^a NOVARTIS PHARMA AG   (Switzerland)

^b MONOGRAM BIOSCIENCES   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS PROTEIN;

ACCESS TO INFORMATION; ARTICLE; BIOTECHNOLOGY; COMPARATIVE STUDY; COMPUTER PROGRAM; CONTROLLED STUDY; GENOTYPE; HEPATITIS B VIRUS; HEPATITIS C VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; INFORMATION PROCESSING; INFORMATION SYSTEM; INTERNET; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

ALGORITHMS; COMPUTER GRAPHICS; DNA, VIRAL; GENES, VIRAL; GENOME, VIRAL; GENOTYPE; HEPACIVIRUS; HEPATITIS B VIRUS; HIV-1; INTERNET; MOLECULAR SEQUENCE DATA; RECOMBINATION, GENETIC; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE; USER-COMPUTER INTERFACE; VIRUSES;

HEPATITIS B VIRUS; HEPATITIS C VIRUS; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 3142681466     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh419     Document Type: Article

References (19)

1. Sturmer,M., Doerr,H.W. and Preiser,W. (2003) Variety of interpretation systems for human immunodeficiency virus type 1 genotyping: confirmatory information or additional confusion? Curr. Drug Targets Infect. Disord., 3, 373-382.
2. Parkin,N.T. and Schapiro,J.M. (2004) Antiretroviral drug resistance in non-subtype B HIV-1, HIV-2 and SIV. Antiviral Therapy, 9, 3-12.
3. Tsubota,A., Arase,Y., Ren,F., Tanaka,H., Ikeda,K. and Kumada,H. (2001) Genotype may correlate with liver carcinogenesis and tumor characteristics in cirrhotic patients infected with hepatitis B virus subtype adw. J. Med. Virol., 65, 257-265.
4. National Institutes of Health Consensus Development Conference Statement (2002) Management of hepatitis C 2002 (June 10-12, 2002). Gastroenterology, 123, 2082-2099.
5. Siepel,A.C., Halpern,A.L., Macken,C. and Korber,B.T. (1995) A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences. AIDS Res. Hum. Retroviruses, 11, 1413-1416.
6. Salminen,M.O., Carr,J.K., Burke,D.S. and McCutchan,F.E. (1995) Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res. Hum. Retroviruses, 11, 1423-1425.
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. (1999) Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol., 73, 152-160.
8. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 26, 3986-3991.
9. Coffin,J.M., Hughes,S.H. and Varmus,H.E. (1997) Retroviruses. Cold Spring Harbor Laboratory Press, Plainview, NY.
10. Leitner,T., Korber,B., Robertson,D.L., Gao,F. and Hahn,B.H. (1997) Updated proposal of reference sequences of HIV-1 genetic subtypes. In Korber,B., Hahn,B.H, Foley,B., Mellors,J.W., Leitner,T., Meyers,G., McCutchan,F.E. and Kuiken,C.L. (eds) Human Retroviruses and AIDS: A Compilation and Analysis of Nucleic Acid and Amino acid Sequences. Los Alamos National Laboratory, Los Alamos, NM, pp. 1-6.
11. Robertson,B., Myers,G., Howard,C., Brettin,T., Bukh,J., Gaschen,B., Gojobori,J., Maertens,G., Mizokami,M., Nainan,O., Netesov,S., Nishioka,K., Shin-i,T., Simmonds,P., Smith,D., Stuyver,L. and Weiner,A. (1998) Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: proposals for standardization. International Committee on Virus Taxonomy. Arch. Virol., 143, 2493-2503.
12. van Regenmortel,M.H.V., Fauquet,C.M, Bishop,D.H.L., Carstens,E.B., Estes,M.K., Lemon,S.M., Maniloff,J., Mayo,M.A., McGeoch,D.J., Pringle,C.R. and Wickner,R.B. (2000) Virus Taxonomy. Seventh report of the International Committee on Taxonomy of Viruses. Academic Press, New York.
13. Kalinina,O., Norder,H., Mukomolov,S. and Magnius,L.O. (2002) A natural intergenotypic recombinant of Hepatitis C virus identified in St. Petersburg. J. Virol., 76, 4034-4043.
14. Arauz-Ruiz,P., Norder,H., Robertson,B.H. and Magnius,L.O. (2002) Genotype H: a new Amerindian genotype of hepatitis B virus revealed in Central America. J. Gen. Virol., 83, 2059-2073.
15. Brown,B., Oberste,M.S., Maher,K. and Pallansch,M.A. (2003) Complete genomic sequencing shows that polioviruses and members of human enterovirus species C are closely related in the noncapsid coding region. J. Virol., 77, 8973-8984.
16. Carr,J.K., Salminen,M.O., Albert,J., Sanders-Buell,E., Gotte,D., Birx,D.L. and McCutchan,F.E. (1998) Full genome sequences of human immunodeficiency virus type 1 subtypes G and A/G intersubtype recombinants. Virology, 247, 22-31.
17. Gao,F., Robertson,D.L., Morrison,S.G., Hui,H., Craig,S., Decker,J., Fultz,P.N., Girard,M., Shaw,G.M., Hahn,B.H. and Sharp,P.M. (1996) The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin. J. Virol., 70, 7013-7029.
18. Yanagi,M., Purcell,R.H., Emerson,S.U. and Bukh,J. (1999) Hepatitis C virus: an infectious molecular clone of a second major genotype (2a) and lack of viability of intertypic 1a and 2a chimeras. Virology, 262, 250-263.
19. Grassly,N.C. and Holmes,E.C. (1997) A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol. Biol. Evol., 14, 239-247.