VIGOR, an annotation program for small viral genomes

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Wang, Shiliang ^a   Sundaram, Jaideep P ^a,b   Spiro, David ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

^b GEORGETOWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOME ANNOTATION; INFECTIOUS DISEASE; OPEN READING FRAME; PARALLEL SEQUENCING; PRODUCTION PIPELINES; PROTEIN CODING REGIONS; PROTEIN-CODING GENES; SEQUENCE SIMILARITY;

DISEASES; FORECASTING; PROTEINS; RNA; VIRUSES;

GENES;

CORONAVIRUS; ORTHOMYXOVIRIDAE; RHINOVIRUS; RNA VIRUSES; ROTAVIRUS; SARS CORONAVIRUS;

ARTICLE; BIOLOGY; COMPUTER PROGRAM; GENETIC DATABASE; GENETICS; METHODOLOGY; MOLECULAR GENETICS; OPEN READING FRAME; ORTHOMYXOVIRUS; START CODON; STOP CODON; VIRUS GENOME;

CODON, INITIATOR; CODON, TERMINATOR; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENOME, VIRAL; MOLECULAR SEQUENCE ANNOTATION; OPEN READING FRAMES; ORTHOMYXOVIRIDAE; SOFTWARE;

EID: 77956486571     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-451     Document Type: Article

References (30)

1. Borodovsky M, Rudd KE, Koonin EV. Intrinsic and extrinsic approaches for detecting genes in a bacterial genome. Nucleic Acids Res 1994, 22(22):4756-4767. 10.1093/nar/22.22.4756, 308528, 7984428.
2. Mills R, Rozanov M, Lomsadze A, Tatusova T, Borodovsky M. Improving gene annotation of complete viral genomes. Nucleic Acids Res 2003, 31(23):7041-7055. 10.1093/nar/gkg878, 290248, 14627837.
3. Besemer J, Borodovsky M. Heuristic approach to deriving models for gene finding. Nucleic Acids Res 1999, 27(19):3911-3920. 10.1093/nar/27.19.3911, 148655, 10481031.
4. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
5. Mount SM. A catalogue of splice junction sequences. Nucleic Acids Res 1982, 10(2):459-472. 10.1093/nar/10.2.459, 326150, 7063411.
6. Ziebuhr J. Molecular biology of severe acute respiratory syndrome coronavirus. Curr Opin Microbiol 2004, 7(4):412-419. 10.1016/j.mib.2004.06.007, 15358261.
7. Dos Ramos F, Carrasco M, Doyle T, Brierley I. Programmed -1 ribosomal frameshifting in the SARS coronavirus. Biochem Soc Trans 2004, 32(Pt 6):1081-1083.
8. Horimoto T, Kawaoka Y. Influenza: lessons from past pandemics, warnings from current incidents. Nat Rev Microbiol 2005, 3(8):591-600. 10.1038/nrmicro1208, 16064053.
9. Nicholson KG, Wood JM, Zambon M. Influenza. Lancet 2003, 362(9397):1733-1745. 10.1016/S0140-6736(03)14854-4, 14643124.
10. Gradi A, Svitkin YV, Sommergruber W, Imataka H, Morino S, Skern T, Sonenberg N. Human rhinovirus 2A proteinase cleavage sites in eukaryotic initiation factors (eIF) 4GI and eIF4GII are different. J Virol 2003, 77(8):5026-5029. 10.1128/JVI.77.8.5026-5029.2003, 152112, 12663812.
11. Deming DJ, Graham RL, Denison MR, Baric RS. Processing of open reading frame 1a replicase proteins nsp7 to nsp10 in murine hepatitis virus strain A59 replication. J Virol 2007, 81(19):10280-10291. 10.1128/JVI.00017-07, 2045455, 17634238.
12. Graham RL, Denison MR. Replication of murine hepatitis virus is regulated by papain-like proteinase 1 processing of nonstructural proteins 1, 2, and 3. J Virol 2006, 80(23):11610-11620. 10.1128/JVI.01428-06, 1642617, 16971428.
13. Kiemer L, Lund O, Brunak S, Blom N. Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology. BMC Bioinformatics 2004, 5:72. 10.1186/1471-2105-5-72, 442122, 15180906.
14. Guo FB, Zhang CT. ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes. BMC Bioinformatics 2006, 7:9. 10.1186/1471-2105-7-9, 1352377, 16401352.
15. Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Tatusova T. FLAN: a web server for influenza virus genome annotation. Nucleic Acids Res 2007, (35 Web Server):W280-284. 10.1093/nar/gkm354, 1933127, 17545199.
16. Steinhauer DA, Skehel JJ. Genetics of influenza viruses. Annu Rev Genet 2002, 36:305-332. 10.1146/annurev.genet.36.052402.152757, 12429695.
17. Chen W, Calvo PA, Malide D, Gibbs J, Schubert U, Bacik I, Basta S, O'Neill R, Schickli J, Palese P, et al. A novel influenza A virus mitochondrial protein that induces cell death. Nat Med 2001, 7(12):1306-1312. 10.1038/nm1201-1306, 11726970.
18. Estes MK, Kang G, Zeng CQ, Crawford SE, Ciarlet M. Pathogenesis of rotavirus gastroenteritis. Novartis Found Symp 2001, 238:82-96. discussion 96-100, full_text, 11444037.
19. Matthijnssens J, Ciarlet M, Heiman E, Arijs I, Delbeke T, McDonald SM, Palombo EA, Iturriza-Gomara M, Maes P, Patton JT, et al. Full genome-based classification of rotaviruses reveals a common origin between human Wa-Like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains. J Virol 2008, 82(7):3204-3219. 10.1128/JVI.02257-07, 2268446, 18216098.
20. Kistler AL, Webster DR, Rouskin S, Magrini V, Credle JJ, Schnurr DP, Boushey HA, Mardis ER, Li H, DeRisi JL. Genome-wide diversity and selective pressure in the human rhinovirus. Virol J 2007, 4:40. 10.1186/1743-422X-4-40, 1892812, 17477878.
21. Palmenberg AC, Spiro D, Kuzmickas R, Wang S, Djikeng A, Rathe JA, Fraser-Liggett CM, Liggett SB. Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution. Science 2009, 324(5923):55-59. 10.1126/science.1165557, 19213880.
22. Zhang X, Hasoksuz M, Spiro D, Halpin R, Wang S, Vlasova A, Janies D, Jones LR, Ghedin E, Saif LJ. Quasispecies of bovine enteric and respiratory coronaviruses based on complete genome sequences and genetic changes after tissue culture adaptation. Virology 2007, 363(1):1-10. 10.1016/j.virol.2007.03.018, 17434558.
23. Hasoksuz M, Alekseev K, Vlasova A, Zhang X, Spiro D, Halpin R, Wang S, Ghedin E, Saif LJ. Biologic, antigenic, and full-length genomic characterization of a bovine-like coronavirus isolated from a giraffe. J Virol 2007, 81(10):4981-4990. 10.1128/JVI.02361-06, 1900194, 17344285.
24. Zhang X, Hasoksuz M, Spiro D, Halpin R, Wang S, Stollar S, Janies D, Hadya N, Tang Y, Ghedin E, et al. Complete genomic sequences, a key residue in the spike protein and deletions in nonstructural protein 3b of US strains of the virulent and attenuated coronaviruses, transmissible gastroenteritis virus and porcine respiratory coronavirus. Virology 2007, 358(2):424-435. 10.1016/j.virol.2006.08.051, 1850758, 17023013.
25. Alekseev KP, Vlasova AN, Jung K, Hasoksuz M, Zhang X, Halpin R, Wang S, Ghedin E, Spiro D, Saif LJ. Bovine-like coronaviruses isolated from four species of captive wild ruminants are homologous to bovine coronaviruses, based on complete genomic sequences. J Virol 2008, 82(24):12422-12431. 10.1128/JVI.01586-08, 2593316, 18842722.
26. Li W, Shi Z, Yu M, Ren W, Smith C, Epstein JH, Wang H, Crameri G, Hu Z, Zhang H, et al. Bats are natural reservoirs of SARS-like coronaviruses. Science 2005, 310(5748):676-679. 10.1126/science.1118391, 16195424.
27. Zhang J, Liu Y, Hu L, Gao Q, Zhang Z, Zhang X, Chen J, Gong X, Song L, Liu Y, et al. Preparation and characterization of SARS in-house reference antiserum. Vaccine 2005, 23(48-49):5666-5669. 10.1016/j.vaccine.2004.12.032, 16269206.
28. Chen LL, Ou HY, Zhang R, Zhang CT. ZCURVE_CoV: a new system to recognize protein coding genes in coronavirus genomes, and its applications in analyzing SARS-CoV genomes. Biochem Biophys Res Commun 2003, 307(2):382-388. 10.1016/S0006-291X(03)01192-6, 12859968.
29. Sharma R, Maheshwari JK, Prakash T, Dash D, Brahmachari SK. Recognition and analysis of protein-coding genes in severe acute respiratory syndrome associated coronavirus. Bioinformatics 2004, 20(7):1074-1080. 10.1093/bioinformatics/bth041, 14764577.
30. McDonald SM, Matthijnssens J, McAllen JK, Hine E, Overton L, Wang S, Lemey P, Zeller M, Van Ranst M, Spiro DJ, et al. Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations. PLoS Pathog 2009, 5(10):e1000634. 10.1371/journal.ppat.1000634, 2760143, 19851457.