ViPTree: The viral proteomic tree server

Bioinformatics

Volumn 33, Issue 15, 2017, Pages 2379-2380

  Nishimura, Yosuke ^a   Yoshida, Takashi ^a   Kuronishi, Megumi ^a   Uehara, Hideya ^b   Ogata, Hiroyuki ^a   Goto, Susumu ^a  

^a KYOTO UNIVERSITY   (Japan)

^b HEWLETT PACKARD ENTERPRISE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VIRAL PROTEIN;

CLASSIFICATION; GENETICS; GENOMICS; METAGENOME; METAGENOMICS; MOLECULAR GENETICS; PROCEDURES; PROTEOMICS; SOFTWARE; VIRUS; VIRUS GENOME;

GENOME, VIRAL; GENOMICS; METAGENOME; METAGENOMICS; MOLECULAR SEQUENCE ANNOTATION; PROTEOMICS; SOFTWARE; VIRAL PROTEINS; VIRUSES;

EID: 85026346250     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btx157     Document Type: Article

References (21)

1. Adriaenssens, E.M. et al. (2015) Integration of genomic and proteomic analyses in the classification of the Siphoviridae family. Virology, 477, 144-154.
2. Bellas, C.M. et al. (2015) Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions. Front. Microbiol., 6, 656.
3. Bhunchoth, A. et al. (2016) Two asian jumbo phages, URSL2 and URSF1, infect Ralstonia solanacearum and show common features of UKZ-related phages. Virology, 494, 56-66.
4. Bostock, M. et al. (2011) (3): Data-Driven Documents. IEEE Trans. Vis Comput. Graph., 17, 2301-2309.
5. Edwards, R.A. and Rohwer, F. (2005) Viral metagenomics. Nat. Rev., 3, 504-510.
6. Fuhrman, J.A. (1999) Marine viruses and their biogeochemical and ecological effects. Nature, 399, 541-548.
7. Glazko, G. et al. (2007) Evolutionary history of bacteriophages with doublestranded DNA genomes. Biol. Direct., 2, 36.
8. Iranzo, J. et al. (2016) Bipartite network analysis of the archaeal virosphere: evolutionary connections between viruses and capsidless mobile elements. J. Virol., 90, 11043-11055.
9. Iranzo, J. et al. (2016) The double-stranded DNA virosphere as a modular hierarchical network of gene sharing. MBio, 7, e00978-e00916.
10. Lavigne, R. et al. (2009) Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiol., 9, 224.
11. Lavigne, R. et al. (2008) Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools. Res. Microbiol, 159, 406-414.
12. Lima-Mendez, G. et al. (2008) Reticulate representation of evolutionary and functional relationships between phage genomes. Mol Biol Evol, 25, 762-777.
13. Mihara, T. et al. (2016) Linking Virus Genomes with Host Taxonomy. Viruses, 8, 66.
14. Mizuno, C.M. et al. (2013) Expanding the marine virosphere using metagenomics. PLoS Genet., 9, e1003987.
15. Nishimura, Y. et al. (2017) Environmental viral genomes shed new light on virus-host interactions in the ocean. mSphere, 2, e00359-16.
16. Paez-Espino, D. et al. (2016) Uncovering Earth's virome. Nature, 536, 425-430.
17. Rohwer, F., and Edwards, R. (2002) The Phage Proteomic Tree: a genomebased taxonomy for phage. J. Bacteriol., 184, 4529-4535.
18. Roux, S. et al. (2016) Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature, 537, 689-693.
19. Roux, S. et al. (2015) Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. Elife, 4, e08490.
20. Suttle, C.A. (2005) Viruses in the sea. Nature, 437, 356-361.
21. Wu, G.A. et al. (2009) Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method. Proc. Natl. Acad. Sci. USA, 106, 12826-12831.