Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification

Archives of Virology

Volumn 159, Issue 12, 2014, Pages 3293-3304

  Bao, Yiming ^a   Chetvernin, Vyacheslav ^a   Tatusova, Tatiana ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; CLASSIFICATION; GENETICS; INTERNET; NATIONAL HEALTH ORGANIZATION; PROCEDURES; SEQUENCE HOMOLOGY; UNITED STATES; VIRUS; VIRUS GENOME;

COMPUTATIONAL BIOLOGY; GENOME, VIRAL; INTERNET; NATIONAL INSTITUTES OF HEALTH (U.S.); SEQUENCE HOMOLOGY; UNITED STATES; VIRUSES;

EID: 84922394370     PISSN: 03048608     EISSN: 14328798     Source Type: Journal    
DOI: 10.1007/s00705-014-2197-x     Document Type: Article

References (34)

1. Bao Y, Federhen S, Leipe D, Pham V, Resenchuk S, Rozanov M, Tatusov R, Tatusova T (2004) National center for biotechnology information viral genomes project. J Virol 78:7291–7298
2. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (2011) Virus taxonomy—ninth report of the International Committee on Taxonomy of viruses. Elsevier/Academic Press, London
3. Lauber C, Gorbalenya AE (2012) Partitioning the genetic diversity of a virus family: approach and evaluation through a case study of picornaviruses. J Virol 86:3890–3904
4. Lauber C, Gorbalenya AE (2012) Genetics-based classification of filoviruses calls for expanded sampling of genomic sequences. Viruses 4:1425–1437
5. Deng M, Yu C, Liang Q, He RL, Yau SS (2011) A novel method of characterizing genetic sequences: genome space with biological distance and applications. PLoS One 6:e17293. doi:10.1371/journal.pone.0017293
6. Yu C, Hernandez T, Zheng H, Yau SC, Huang HH, He RL, Yang J, Yau SS (2013) Real time classification of viruses in 12 dimensions. PLoS One 8:e64328. doi:10.1371/journal.pone.0064328
7. González JM, Gomez-Puertas P, Cavanagh D, Gorbalenya AE, Enjuanes L (2003) A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae. Arch Virol 148:2207–2235
8. Fauquet CM, Briddon RW, Brown JK, Moriones E, Stanley J, Zerbini M, Zhou X (2008) Geminivirus strain demarcation and nomenclature. Arch Virol 153:783–821
9. Muhire B, Martin DP, Brown JK, Navas-Castillo J, Moriones E, Zerbini FM, Rivera-Bustamante R, Malathi VG, Briddon RW, Varsani A (2013) A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Arch Virol 158:1411–1424
10. Varsani A, Martin DP, Navas-Castillo J, Moriones E, Hernández-Zepeda C, Idris A, Murilo Zerbini F, Brown JK (2014) Revisiting the classification of curtoviruses based on genome-wide pairwise identity. Arch Virol
11. Bernard HU, Burk RD, Chen Z, van Doorslaer K, Hausen H, de Villiers EM (2010) Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments. Virology 25:70–79
12. Oberste MS, Maher K, Kilpatrick DR, Pallansch MA (1999) Molecular evolution of the human enteroviruses: correlation of serotype with VP1 sequence and application to picornavirus classification. J Virol 73:1941–1948
13. Adams MJ, Antoniw JF, Fauquet CM (2005) Molecular criteria for genus and species discrimination within the family Potyviridae. Arch Virol 150:459–479
14. Matthijnssens J, Ciarlet M, Heiman E, Arijs I, Delbeke T, McDonald SM, Palombo EA, Iturriza-Gómara M, Maes P, Patton JT, Rahman M, Van Ranst M (2008) 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 82:3204–3219
15. Bao Y, Kapustin Y, Tatusova T (2008) Virus classification by pairwise sequence comparison (PASC). In: Mahy BWJ, Van Regenmortel MHV (eds) Encyclopedia of virology, vol 5, 3rd edn. Elsevier, Oxford, pp 342–348
16. Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48:443–453
17. Myers EW, Miller W (1988) Optimal alignment in linear space Comp. Appl Biosci 4:11–17
18. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
19. Bao Y, Chetvernin V, Tatusova T (2012) PAirwise sequence comparison (PASC) and its application in the classification of filoviruses. Viruses 4:1318–1327
20. Scholl D, Kieleczawa J, Kemp P, Rush J, Richardson CC, Merril C, Adhya S, Molineux IJ (2004) Genomic analysis of bacteriophages SP6 and K1-5, an estranged subgroup of the T7 supergroup. J Mol Biol 335:1151–1171
21. Lavigne R, Seto D, Mahadevan P, Ackermann HW, Kropinski AM (2008) Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools. Res Microbiol 159:406–414
22. Cuellar WJ, De Souza J, Barrantes I, Fuentes S, Kreuze JF (2011) Distinct cavemoviruses interact synergistically with sweet potato chlorotic stunt virus (genus Crinivirus) in cultivated sweet potato. J Gen Virol 92:1233–1243
23. Domínguez M, Ramos PL, Sánchez Y, Crespo J, Andino V, Pujol M, Borroto C (2009) Tobacco mottle leaf curl virus, a new begomovirus infecting tobacco in Cuba. Plant Pathol 58:786
24. Huang YW, Ni YY, Dryman BA, Meng XJ (2010) Multiple infection of porcine Torque teno virus in a single pig and characterization of the full-length genomic sequences of four U.S. prototype PTTV strains: implication for genotyping of PTTV. Virology 396:289–297
25. Lam N, Creamer R, Rascon J, Belfon R (2009) Characterization of a new curtovirus, pepper yellow dwarf virus, from chile pepper and distribution in weed hosts in New Mexico. Arch Virol 154:429–436
26. Li J, Pan Y, Deng Q, Cai H, Ke Y (2013) Identification and characterization of eleven novel human gamma-papillomavirus isolates from healthy skin, found at low frequency in a normal population. PLoS One 8:e77116. doi:10.1371/journal.pone.0077116
27. Li R, Gao S, Hernandez AG, Wechter WP, Fei Z, Ling KS (2012) Deep sequencing of small RNAs in tomato for virus and viroid identification and strain differentiation. PLoS One 7:e37127. doi:10.1371/journal.pone.0037127
28. Mubin M, Briddon RW, Mansoor S (2009) Diverse and recombinant DNA betasatellites are associated with a begomovirus disease complex of Digera arvensis, a weed host. Virus Res 142:208–212
29. Shafiq M, Asad S, Zafar Y, Briddon RW, Mansoor S (2010) Pepper leaf curl Lahore virus requires the DNA B component of Tomato leaf curl New Delhi virus to cause leaf curl symptoms. Virol J 7:367
30. Vaira AM, Maroon-Lango CJ, Hammond J (2008) Molecular characterization of Lolium latent virus, proposed type member of a new genus in the family Flexiviridae. Arch Virol 153:1263–1270
31. Wylie S, Jones M (2011) Hardenbergia virus A, a novel member of the family Betaflexiviridae from a wild legume in Southwest Australia. Arch Virol 156:1245–1250
32. Wylie SJ, Li H, Jones MG (2013) Donkey orchid symptomless virus: a viral ‘platypus’ from Australian terrestrial orchids. PLoS One 8:e79587. doi:10.1371/journal.pone.0079587
33. Yan ZL, Song LM, Zhou T, Zhang YJ, Li MF, Li HF, Fan ZF (2010) Identification and molecular characterization of a new potyvirus from Panax notoginseng. Arch Virol 155:949–957
34. Zaffalon V, Mukherjee SK, Reddy VS, Thompson JR, Tepfer M (2012) A survey of geminiviruses and associated satellite DNAs in the cotton-growing areas of northwestern India. Arch Virol 157:483–495