The RNA Virus Database

Nucleic Acids Research

Volumn 37, Issue SUPPL. 1, 2009, Pages

  Belshaw, Robert ^a   de Oliveira, Tulio ^a,b   Markowitz, Sidney ^c   Rambaut, Andrew ^d  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF THE WESTERN CAPE   (South Africa)

^c UNIVERSITY OF AUCKLAND   (New Zealand)

^d UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENOMICS; INFORMATION PROCESSING; INFORMATION SERVICE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; RNA VIRUS; RNA VIRUS DATABASE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; TAXONOMY; VIRUS GENOME;

BASE SEQUENCE; DATABASES, NUCLEIC ACID; GENES, VIRAL; GENOME, VIRAL; GENOMICS; RNA VIRUSES; SEQUENCE ALIGNMENT;

RNA VIRUSES;

EID: 58149195098     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn729     Document Type: Article

References (19)

1. Belshaw,R., Gardner,A., Rambaut,A. and Pybus,O.G. (2008) Pacing a small cage: Mutation and RNA viruses. Trends Ecol. Evol., 23, 188-193.
2. Sleigh,A. (2005) Twenty-.rst century plague: The story of SARS. Nature, 435, 886-887.
3. Rambaut,A., Posada,D., Crandall,K.A. and Holmes,E.C. (2004) The causes and consequences of HIV evolution. Nat. Rev. Genet., 5, 52-61.
4. Kuiken,T., Holmes,E.C., McCauley,J., Rimmelzwaan,G.F., Williams,C.S. and Grenfell,B.T. (2006) Host species barriers to influenza virus infections. Science, 312, 394-397.
5. Wolfe,N.D., Dunavan,C.P. and Diamond,J. (2007) Origins of major human infectious diseases. Nature, 447, 279-283.
6. Gorbalenya,A.E. (2001) Big nidovirus genome - when count and order of domains matter. Adv. Exp. Med. Biol., 494, 1-17.
7. Le Gall,O., Christian,P., Fauquet,C.M., King,A.M.Q., Knowles,N.J., Nakashima,N., Stanway,G. and Gorbalenya,A.E. (2008) Picornavirales, a proposed order of positive-sense single-stranded RNA viruses with a pseudo-T=3 virion architecture. Arch. Virol., 153, 715-727.
8. Koonin,E.V. and Dolja,V.V. (1993) Evolution and taxonomy of positive-strand RNA vruses - implications of comparative-analysis of amino acid sequences. Crit. Rev. Biochem. Mol. Biol., 28, 375-430.
9. Zanotto,P.M.D., Gibbs,M.J., Gould,E.A. and Holmes,E.C. (1996) A reevaluation of the higher taxonomy of viruses based on RNA polymerases. J. Virol., 70, 6083-6096.
10. Hausmann,S., Garcin,D., Delenda,C. and Kolakofsky,D. (1999) The versatility of paramyxovirus RNA polymerase stuttering. J. Virol., 73, 5568-5576.
11. Stajich,J.E., Block,D., Boulez,K., Brenner,S.E., Chervitz,S.A., Dagdigian,C., Fuellen,G., Gilbert,J.G.R., Korf,I., Lapp,H. et al. (2002) The bioperl toolkit: Perl modules for the life sciences. Genome Res., 12, 1611-1618.
12. Belshaw,R. and Katzourakis,A. (2005) BlastAlign: A program that uses blast to align problematic nucleotide sequences. Bioinformatics, 21, 122-123.
13. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) Clustal-W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
14. Swofford, D. (1998) PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods) Version 4. Sinauer, Sunderland, MA.
15. Mueller,J. and Mueller,K. (2004) TREEGRAPH: Automated drawing of complex tree figures using an extensible tree description format. Mol. Ecol. Notes, 4, 786-788.
16. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic Local Alignment Search Tool. J. Mol. Biol., 215, 403-410.
17. Belshaw,R., Pybus,O.G. and Rambaut,A. (2007) The evolution of genome compression and genomic novelty in RNA viruses. Genome Res., 17 1496-1504.
18. van Regenmortel,M.H.V., Fauquet,C.M., Bishop,D.H.L., Carstens,E.B., Estes,M.K., Lemon,S.M., Manilo.,J., Mayo,M.A., McGeoch,D.J., Pringle,C.R. et al. (2000) Virus Taxonomy: Classification and Nomenclature of Viruses. Academic Press, San Diego, CA.
19. Pruitt,K.D., Tatusova,T. and Maglott,D.R. (2005) NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 33, D501-D504.