NCBI viral Genomes resource

Nucleic Acids Research

Volumn 43, Issue D1, 2015, Pages D571-D577

  Brister, J Rodney ^a   Ako Adjei, Danso ^a   Bao, Yiming ^a   Blinkova, Olga ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENETIC DATABASE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; VIRUS DETECTION; VIRUS GENOME; VIRUS IDENTIFICATION; CLASSIFICATION; COMPUTER PROGRAM; HIGH THROUGHPUT SEQUENCING; INTERNET; MOLECULAR GENETICS; NUCLEIC ACID DATABASE; VIRUS;

DATABASES, NUCLEIC ACID; GENOME, VIRAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INTERNET; MOLECULAR SEQUENCE ANNOTATION; SOFTWARE; VIRUSES;

EID: 84941073363     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1207     Document Type: Article

References (57)

1. Baize, S., Pannetier, D., Oestereich, L., Rieger, T., Koivogui, L., Magassouba, N., Soropogui, B., Sow, M. S., Keita, S., De Clerck, H. et al. (2014) Emergence of Zaire Ebola virus disease in Guinea-preliminary report. N. Engl. J. Med., 371, 1418-1425.
2. Gire, S. K., Goba, A., Andersen, K. G., Sealfon, R. S., Park, D. J., Kanneh, L., Jalloh, S., Momoh, M., Fullah, M., Dudas, G. et al. (2014) Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science, 345, 1369-1372.
3. Haagmans, B. L., Al Dhahiry, S. H., Reusken, C. B., Raj, V. S., Galiano, M., Myers, R., Godeke, G. J., Jonges, M., Farag, E., Diab, A. et al. (2014) Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation. Lancet Infect. Dis., 14, 140-145.
4. Cotten, M., Watson, S. J., Kellam, P., Al-Rabeeah, A. A., Makhdoom, H. Q., Assiri, A., Al-Tawfq, J. A., Alhakeem, R. F., Madani, H., AlRabiah, F. A. et al. (2013) Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study. Lancet, 382, 1993-2002.
5. Karsch-Mizrachi, I., Nakamura, Y., Cochrane, G. and International, Nucleotide Sequence Database Collaboration. (2012) The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res., 40, D33-D37.
6. Benson, D. A., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. and Sayers, E. W. (2014) GenBank. Nucleic Acids Res., 42, D32-D37.
7. Brooksbank, C., Bergman, M. T., Apweiler, R., Birney, E. and Thornton, J. (2014) The European Bioinformatics Institute's data resources 2014. Nucleic Acids Res., 42, D18-D25.
8. Kosuge, T., Mashima, J., Kodama, Y., Fujisawa, T., Kaminuma, E., Ogasawara, O., Okubo, K., Takagi, T. and Nakamura, Y. (2014) DDBJ progress report: a new submission system for leading to a correct annotation. Nucleic Acids Res., 42, D44-D49.
9. Masson, P., Hulo, C., De Castro, E., Bitter, H., Gruenbaum, L., Essioux, L., Bougueleret, L., Xenarios, I. and Le Mercier, P. (2013) ViralZone: recent updates to the virus knowledge resource. Nucleic Acids Res., 41, D579-D583.
10. Pruitt, K. D., Tatusova, T. and Maglott, D. R. (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65.
11. Bao, Y., Bolotov, P., Dernovoy, D., Kiryutin, B. and Tatusova, T. (2007) FLAN: a web server for infuenza virus genome annotation. Nucleic Acids Res., 35, W280-W284.
12. Wang, S., Sundaram, J. P. and Stockwell, T. B. (2012) VIGOR extended to annotate genomes for additional 12 different viruses. Nucleic Acids Res., 40, W186-W192.
13. Wang, S., Sundaram, J. P. and Spiro, D. (2010) VIGOR, an annotation program for small viral genomes. BMC Bioinformatics, 11, 451.
14. Borozan, I., Watt, S. N. and Ferretti, V. (2013) Evaluation of alignment algorithms for discovery and identification of pathogens using RNA-Seq. PLoS One, 8, e76935.
15. Gaynor, A. M., Nissen, M. D., Whiley, D. M., Mackay, I. M., Lambert, S. B., Wu, G., Brennan, D. C., Storch, G. A., Sloots, T. P. and Wang, D. (2007) Identification of a novel polyomavirus from patients with acute respiratory tract infections. PLoS Pathog., 3, e64.
16. Holtz, L. R., Finkbeiner, S. R., Zhao, G., Kirkwood, C. D., Girones, R., Pipas, J. M. and Wang, D. (2009) Klassevirus 1, a previously undescribed member of the family Picornaviridae, is globally widespread. Virol. J., 6, 86.
17. Dutilh, B. E., Cassman, N., McNair, K., Sanchez, S. E., Silva, G. G., Boling, L., Barr, J. J., Speth, D. R., Seguritan, V., Aziz, R. K. et al. (2014) A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat. Commun., 5, 4498.
18. Cotten, M., Petrova, V., Phan, M. V., Rabaa, M. A., Watson, S. J., Ong, S. H., Kellam, P. and Baker, S. (2014) Deep sequencing of norovirus genomes defnes evolutionary patterns in an urban tropical setting. J. Virol., 88, 11056-11069.
19. Dennis, A. F., McDonald, S. M., Payne, D. C., Mijatovic-Rustempasic, S., Esona, M. D., Edwards, K. M., Chappell, J. D. and Patton, J. T. (2014) Molecular epidemiology of contemporary G2P[4] human rotaviruses cocirculating in a single U. S.community: footprints of a globally transitioning genotype. J. Virol., 88, 3789-3801.
20. Reyes, A., Semenkovich, N. P., Whiteson, K., Rohwer, F. and Gordon, J. I. (2012) Going viral: next-generation sequencing applied to phage populations in the human gut. Nat. Rev. Microbiol., 10, 607-617.
21. Kostic, A. D., Ojesina, A. I., Pedamallu, C. S., Jung, J., Verhaak, R. G., Getz, G. and Meyerson, M. (2011) PathSeq: software to identify or discover microbes by deep sequencing of human tissue. Nat. Biotechnol., 29, 393-396.
22. Wang, Q., Jia, P. and Zhao, Z. (2013) VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. PLoS One, 8, e64465.
23. Naccache, S. N., Federman, S., Veeraraghavan, N., Zaharia, M., Lee, D., Samayoa, E., Bouquet, J., Greninger, A. L., Luk, K. C., Enge, B. et al. (2014) A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res., 24, 1180-1192.
24. Bao, Y., Federhen, S., Leipe, D., Pham, V., Resenchuk, S., Rozanov, M., Tatusov, R. and Tatusova, T. (2004) National Center for Biotechnology Information Viral Genomes Project. J. Virol., 78, 7291-7298.
25. Brister, J. R., Bao, Y., Zhdanov, S. A., Ostapchuck, Y., Chetvernin, V., Kiryutin, B., Zaslavsky, L., Kimelman, M. and Tatusova, T. A. (2014) Virus Variation Resource-recent updates and future directions. Nucleic Acids Res., 42, D660-D665.
26. Pruitt, K. D., Tatusova, T., Brown, G. R. and Maglott, D. R. (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res., 40, D130-D135.
27. Mills, R., Rozanov, M., Lomsadze, A., Tatusova, T. and Borodovsky, M. (2003) Improving gene annotation of complete viral genomes. Nucleic Acids Res., 31, 7041-7055.
28. Kattenhorn, L. M., Mills, R., Wagner, M., Lomsadze, A., Makeev, V., Borodovsky, M., Ploegh, H. L. and Kessler, B. M. (2004) Identification of proteins associated with murine cytomegalovirus virions. J. Virol., 78, 11187-11197.
29. Brister, J. R., Le Mercier, P. and Hu, J. C. (2012) Microbial virus genome annotation-mustering the troops to fight the sequence onslaught. Virology, 434, 175-180.
30. Lawrence, J. G., Hatfull, G. F. and Hendrix, R. W. (2002) Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J. Bacteriol., 184, 4891-4905.
31. Pourkarim, M. R., Amini-Bavil-Olyaee, S., Kurbanov, F., Van Ranst, M. and Tacke, F. (2014) Molecular identification of hepatitis B virus genotypes/subgenotypes: revised classification hurdles and updated resolutions. World J. Gastroenterol., 20, 7152-7168.
32. Simmonds, P., Bukh, J., Combet, C., Deleage, G., Enomoto, N., Feinstone, S., Halfon, P., Inchauspe, G., Kuiken, C., Maertens, G. et al. (2005) Consensus proposals for a Unified system of nomenclature of hepatitis C virus genotypes. Hepatology, 42, 962-973.
33. Smith, D. B., Bukh, J., Kuiken, C., Muerhoff, A. S., Rice, C. M., Stapleton, J. T. and Simmonds, P. (2014) Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource. Hepatology, 59, 318-327.
34. Tanwar, S. and Dusheiko, G. (2012) Is there any value to hepatitis B virus genotype analysis? Curr. Gastroenterol. Rep., 14, 37-46.
35. Federhen, S. (2012) The NCBI Taxonomy database. Nucleic Acids Res., 40, D136-D143.
36. Jancovich, J. K., Chinchar, V. G., Hyatt, A., Miyazaki, T., Williams, T. and Zhang, Q. Y. (2012) In: King, AMQ, Adams, MJ, Carstens, EB and Lefkowitz, EJ (eds). Virus Taxonomy: Classification and Nomenclature of Viruses: Ninth Report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press, San Diego, CA.
37. Maan, S., Rao, S., Maan, N. S., Anthony, S. J., Attoui, H., Samuel, A. R. and Mertens, P. P. (2007) Rapid cDNA synthesis and sequencing techniques for the genetic study of bluetongue and other dsRNA viruses. J. Virol. Methods, 143, 132-139.
38. Alfson, K. J., Beadles, M. W. and Griffths, A. (2014) A new approach to determining whole viral genomic sequences including termini using a single deep sequencing run. J. Virol. Methods, 208, 1-5.
39. Davison, A. J. (2010) Herpesvirus systematics. Vet. Microbiol., 143, 52-69.
40. Sabath, N., Wagner, A. and Karlin, D. (2012) Evolution of viral proteins originated de novo by overprinting. Mol. Biol. Evol., 29, 3767-3780.
41. Rancurel, C., Khosravi, M., Dunker, A. K., Romero, P. R. and Karlin, D. (2009) Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation. J. Virol., 83, 10719-10736.
42. Matthijnssens, J., Ciarlet, M., McDonald, S. M., Attoui, H., Banyai, K., Brister, J. R., Buesa, J., Esona, M. D., Estes, M. K., Gentsch, J. R. et al. (2011) Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG). Arch. Virol., 156, 1397-1413.
43. Kuhn, J. H., Bao, Y., Bavari, S., Becker, S., Bradfute, S., Brister, J. R., Bukreyev, A. A., Chandran, K., Davey, R. A., Dolnik, O. et al. (2013) Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae. Arch. Virol., 158, 301-311.
44. Kuhn, J. H., Bao, Y., Bavari, S., Becker, S., Bradfute, S., Brister, J. R., Bukreyev, A. A., Cai, Y., Chandran, K., Davey, R. A. et al. (2013) Virus nomenclature below the species level: a standardized nomenclature for laboratory animal-adapted strains and variants of viruses assigned to the family Filoviridae. Arch. Virol., 158, 1425-1432.
45. UniProt, Consortium. (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res., 38, D142-D148.
46. Pickett, B. E., Sadat, E. L., Zhang, Y., Noronha, J. M., Squires, R. B., Hunt, V., Liu, M., Kumar, S., Zaremba, S., Gu, Z. et al. (2012) ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res., 40, D593-D598.
47. Brister, J. R., Bao, Y., Kuiken, C., Lefkowitz, E. J., Le Mercier, P., Leplae, R., Madupu, R., Scheuermann, R. H., Schobel, S., Seto, D. et al. (2010) Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop. Viruses, 2, 2258-2268.
48. Resch, W., Zaslavsky, L., Kiryutin, B., Rozanov, M., Bao, Y. and Tatusova, T. A. (2009) Virus variation resources at the National Center for Biotechnology Information: dengue virus. BMC Microbiol., 9, 65.
49. Bao, Y., Bolotov, P., Dernovoy, D., Kiryutin, B., Zaslavsky, L., Tatusova, T., Ostell, J. and Lipman, D. (2008) The infuenza virus resource at the National Center for Biotechnology Information. J. Virol., 82, 596-601.
50. Rozanov, M., Plikat, U., Chappey, C., Kochergin, A. and Tatusova, T. (2004) A web-based genotyping resource for viral sequences. Nucleic Acids Res., 32, W654-W659.
51. Fu, W., Sanders-Beer, B. E., Katz, K. S., Maglott, D. R., Pruitt, K. D. and Ptak, R. G. (2009) Human immunodeficiency virus type 1, human protein interaction database at NCBI. Nucleic Acids Res., 37, D417-D422.
52. Bao, Y., Chetvernin, V. and Tatusova, T. (2012) PAirwise Sequence Comparison (PASC) and its application in the classification of floviruses. Viruses, 4, 1318-1327.
53. Bao, Y., Chetvernin, V. and Tatusova, T. (2014) Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification. Arch. Virol., 159, 3293-3304.
54. Boratyn, G. M., Camacho, C., Cooper, P. S., Coulouris, G., Fong, A., Ma, N., Madden, T. L., Matten, W. T., McGinnis, S. D., Merezhuk, Y. et al. (2013) BLAST: a more efficient report with usability improvements. Nucleic Acids Res., 41, W29-W33.
55. Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S. and Madden, T. L. (2008) NCBI BLAST: a better web interface. Nucleic Acids Res., 36, W5-W9.
56. NCBI, Resource Coordinators. (2014) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 42, D7-D17.
57. Klimke, W., Agarwala, R., Badretdin, A., Chetvernin, S., Ciufo, S., Fedorov, B., Kiryutin, B., O'Neill, K., Resch, W., Resenchuk, S. et al. (2009) The National Center for Biotechnology Information's Protein Clusters Database. Nucleic Acids Res., 37, D216-D223.