메뉴 건너뛰기




Volumn 9, Issue 9, 2014, Pages

SDT: A virus classification tool based on pairwise sequence alignment and identity calculation

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BEGOMOVIRUS; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; INTERMETHOD COMPARISON; NONHUMAN; NUCLEOTIDE SEQUENCE; REPRODUCIBILITY; SEQUENCE ALIGNMENT; VIRAL GENETICS; VIRUS GENE; VIRUS GENOME; BIOLOGY; CLASSIFICATION; GENETICS; PROCEDURES; VIRUS;

EID: 84907426295     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0108277     Document Type: Article
Times cited : (1242)

References (46)
  • 1
    • 84893511241 scopus 로고    scopus 로고
    • Towards a taxonomic coherence between average nucleotide identity and 16 S rRNA gene sequence similarity for species demarcation of prokaryotes
    • Kim M, Oh H-S, Park S-C, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16 S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64: 346-351.
    • (2014) Int J Syst Evol Microbiol , vol.64 , pp. 346-351
    • Kim, M.1    Oh, H.-S.2    Park, S.-C.3    Chun, J.4
  • 2
    • 84865370448 scopus 로고    scopus 로고
    • PAirwise Sequence Comparison (PASC) and its application in the classification of filoviruses
    • Bao Y, Chetvernin V, Tatusova T (2012) PAirwise Sequence Comparison (PASC) and its application in the classification of filoviruses. Viruses 4: 1318-1327.
    • (2012) Viruses , vol.4 , pp. 1318-1327
    • Bao, Y.1    Chetvernin, V.2    Tatusova, T.3
  • 3
    • 84878598727 scopus 로고    scopus 로고
    • A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae)
    • Muhire B, Martin DP, Brown JK, Navas-Castillo J, Moriones E, et al. (2013) A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Arch Virol 158: 1411-1424.
    • (2013) Arch Virol , vol.158 , pp. 1411-1424
    • Muhire, B.1    Martin, D.P.2    Brown, J.K.3    Navas-Castillo, J.4    Moriones, E.5
  • 4
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 6
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
    • Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30: 772-780.
    • (2013) Mol Biol Evol , vol.30 , pp. 772-780
    • Katoh, K.1    Standley, D.M.2
  • 8
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
    • (2011) Mol Biol Evol , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5
  • 11
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • Thompson JD, Plewniak F, Poch O (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res 27: 2682-2690.
    • (1999) Nucleic Acids Res , vol.27 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 12
    • 34248374330 scopus 로고    scopus 로고
    • An enhanced RNA alignment benchmark for sequence alignment programs
    • Wilm A, Mainz I, Steger G (2006) An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol Biol 1: 19. doi:10.1186/1748-7188-1-19.
    • (2006) Algorithms Mol Biol , vol.1 , pp. 19
    • Wilm, A.1    Mainz, I.2    Steger, G.3
  • 13
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33: 511-518.
    • (2005) Nucleic Acids Res , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 14
    • 84876220535 scopus 로고    scopus 로고
    • Making automated multiple alignments of very large numbers of protein sequences
    • Sievers F, Dineen D, Wilm A, Higgins DG (2013) Making automated multiple alignments of very large numbers of protein sequences. Bioinformatics 29: 989-995.
    • (2013) Bioinformatics , vol.29 , pp. 989-995
    • Sievers, F.1    Dineen, D.2    Wilm, A.3    Higgins, D.G.4
  • 15
    • 33846197539 scopus 로고    scopus 로고
    • Settling the intractability of multiple alignment
    • Elias I (2006) Settling the intractability of multiple alignment. J Comput Biol 13: 1323-1339.
    • (2006) J Comput Biol , vol.13 , pp. 1323-1339
    • Elias, I.1
  • 16
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • 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.
    • (1970) J Mol Biol , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 17
    • 0003991673 scopus 로고    scopus 로고
    • Sunderland, Massachusetts: Sinauer Associates, Inc.
    • Felsenstein J (2004) Inferring Phylogenies. Sunderland, Massachusetts: Sinauer Associates, Inc.
    • (2004) Inferring Phylogenies
    • Felsenstein, J.1
  • 19
    • 84861323730 scopus 로고    scopus 로고
    • Partitioning the genetic diversity of a virus family: Approach and evaluation through a case study of picornaviruses
    • 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.
    • (2012) J Virol , vol.86 , pp. 3890-3904
    • Lauber, C.1    Gorbalenya, A.E.2
  • 20
    • 84903612358 scopus 로고    scopus 로고
    • Complete genome sequence of Jacquemontia yellow mosaic virus, a novel begomovirus from Venezuela related to other New World bipartite begomoviruses infecting Convolvulaceae
    • Fiallo-Olivé E, Chirinos DT, Geraud-Pouey F, Moriones E, Navas-Castillo J (2014) Complete genome sequence of Jacquemontia yellow mosaic virus, a novel begomovirus from Venezuela related to other New World bipartite begomoviruses infecting Convolvulaceae. Arch Virol. 159: 1857-1860.
    • (2014) Arch Virol , vol.159 , pp. 1857-1860
    • Fiallo-Olivé, E.1    Chirinos, D.T.2    Geraud-Pouey, F.3    Moriones, E.4    Navas-Castillo, J.5
  • 21
    • 41149115557 scopus 로고    scopus 로고
    • 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
    • Matthijnssens J, Ciarlet M, Heiman E, Arijs I, Delbeke T, et al. (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.
    • (2008) J Virol , vol.82 , pp. 3204-3219
    • Matthijnssens, J.1    Ciarlet, M.2    Heiman, E.3    Arijs, I.4    Delbeke, T.5
  • 23
    • 84899935904 scopus 로고    scopus 로고
    • A distinct strain of chickpea chlorotic dwarf virus (genus Mastrevirus, family Geminiviridae) identified in cotton plants affected by leaf curl disease
    • Manzoor MT, Ilyas M, Shafiq M, Haider MS, Shahid AA, et al. (2014) A distinct strain of chickpea chlorotic dwarf virus (genus Mastrevirus, family Geminiviridae) identified in cotton plants affected by leaf curl disease. Arch Virol. 159: 1217-1221.
    • (2014) Arch Virol , vol.159 , pp. 1217-1221
    • Manzoor, M.T.1    Ilyas, M.2    Shafiq, M.3    Haider, M.S.4    Shahid, A.A.5
  • 24
    • 84885947518 scopus 로고    scopus 로고
    • Response of chickpea genotypes to Agrobacterium-mediated delivery of Chickpea chlorotic dwarf virus (CpCDV) genome and identification of resistance source
    • Kanakala S, Verma HN, Vijay P, Saxena DR, Malathi VG (2013) Response of chickpea genotypes to Agrobacterium-mediated delivery of Chickpea chlorotic dwarf virus (CpCDV) genome and identification of resistance source. Appl Microbiol Biotechnol 97: 9491-9501.
    • (2013) Appl Microbiol Biotechnol , vol.97 , pp. 9491-9501
    • Kanakala, S.1    Verma, H.N.2    Vijay, P.3    Saxena, D.R.4    Malathi, V.G.5
  • 25
    • 84905246363 scopus 로고    scopus 로고
    • Begomovirus diversity in tomato crops and weeds in Ecuador and the detection of a recombinant isolate of rhynchosia golden mosaic Yucatan virus infecting tomato
    • Paz-Carrasco LC, Castillo-Urquiza GP, Lima ATM, Xavier CAD, Vivas-Vivas LM, et al. (2014) Begomovirus diversity in tomato crops and weeds in Ecuador and the detection of a recombinant isolate of rhynchosia golden mosaic Yucatan virus infecting tomato. Arch Virol. doi:10.1007/s00705-014-2046-y.
    • (2014) Arch Virol
    • Paz-Carrasco, L.C.1    Castillo-Urquiza, G.P.2    Lima, A.T.M.3    Xavier, C.A.D.4    Vivas-Vivas, L.M.5
  • 26
    • 84907448448 scopus 로고    scopus 로고
    • Isolation and molecular characterization of a distinct begomovirus and its associated betasatellite infecting Hedyotis uncinella (Hook. et Arn.) in Vietnam
    • Du Z, Chen M, Wang Z, Liu Y, Zhang S, et al. (2014) Isolation and molecular characterization of a distinct begomovirus and its associated betasatellite infecting Hedyotis uncinella (Hook. et Arn.) in Vietnam. Virus Genes 80: 246-250.
    • (2014) Virus Genes , vol.80 , pp. 246-250
    • Du, Z.1    Chen, M.2    Wang, Z.3    Liu, Y.4    Zhang, S.5
  • 27
    • 84905226337 scopus 로고    scopus 로고
    • Establishment of three new genera in the family Geminiviridae: Becurtovirus, Eragrovirus and Turncurtovirus
    • Varsani A, Navas-Castillo J, Moriones E, Hernández-Zepeda C, Idris A, et al. (2014) Establishment of three new genera in the family Geminiviridae: Becurtovirus, Eragrovirus and Turncurtovirus. Arch Virol. doi:10.1007/s00705-014-2050-2.
    • (2014) Arch Virol
    • Varsani, A.1    Navas-Castillo, J.2    Moriones, E.3    Hernández-Zepeda, C.4    Idris, A.5
  • 30
    • 84907691813 scopus 로고    scopus 로고
    • A high degree of African streak virus diversity within Nigerian maize fields includes a new mastrevirus species from Axonopus compressus
    • Oluwafemi S, Kraberger S, Shepherd D, Martin D, Varsani A (2014) A high degree of African streak virus diversity within Nigerian maize fields includes a new mastrevirus species from Axonopus compressus. Arch Virol. doi:10.1007/s00705-014-2090-7.
    • (2014) Arch Virol
    • Oluwafemi, S.1    Kraberger, S.2    Shepherd, D.3    Martin, D.4    Varsani, A.5
  • 31
    • 84907704499 scopus 로고    scopus 로고
    • Association of a distinct strain of hollyhock yellow vein mosaic virus and Ludwigia leaf distortion betasatellite with yellow vein mosaic disease of hollyhock (Alcea rosea) in India
    • Srivastava A, S. Kumar S, Raj SK, Pande SS (2014) Association of a distinct strain of hollyhock yellow vein mosaic virus and Ludwigia leaf distortion betasatellite with yellow vein mosaic disease of hollyhock (Alcea rosea) in India. Arch Virol. DOI 10.1007/s00705-014-2108-1.
    • (2014) Arch Virol
    • Srivastava, A.1    Kumar S, S.2    Raj, S.K.3    Pande, S.S.4
  • 32
    • 84900855346 scopus 로고    scopus 로고
    • Pigeon circoviruses display patterns of recombination, genomic secondary structure and selection similar to those of Beak and feather disease viruses
    • Stenzel T, Piasecki T, Chrza¸stek K, Julian L, Muhire BM, et al. (2014) Pigeon circoviruses display patterns of recombination, genomic secondary structure and selection similar to those of Beak and feather disease viruses. J Gen Virol. 95: 1338-1351.
    • (2014) J Gen Virol , vol.95 , pp. 1338-1351
    • Stenzel, T.1    Piasecki, T.2    Chrza¸stek, K.3    Julian, L.4    Muhire, B.M.5
  • 33
    • 84897869818 scopus 로고    scopus 로고
    • Genome Diversity and Evidence of Recombination and Reassortment in Nanoviruses from Europe
    • Grigoras I, Del Cueto Ginzo AI, Martin DP, Varsani A, Romero J, et al. (2014) Genome Diversity and Evidence of Recombination and Reassortment in Nanoviruses from Europe. J Gen Virol.95: 1178-1191.
    • (2014) J Gen Virol , vol.95 , pp. 1178-1191
    • Grigoras, I.1    Del Cueto Ginzo, A.I.2    Martin, D.P.3    Varsani, A.4    Romero, J.5
  • 34
    • 84885306231 scopus 로고    scopus 로고
    • Novel myco-like DNA viruses discovered in the faecal matter of various animals
    • Sikorski A, Massaro M, Kraberger S, Young LM, Smalley D, et al. (2013) Novel myco-like DNA viruses discovered in the faecal matter of various animals. Virus Res 177: 209-216.
    • (2013) Virus Res , vol.177 , pp. 209-216
    • Sikorski, A.1    Massaro, M.2    Kraberger, S.3    Young, L.M.4    Smalley, D.5
  • 36
    • 84896795221 scopus 로고    scopus 로고
    • Isolation and Molecular Characterization of a Novel Picornavirus from Baitfish in the USA
    • Phelps NBD, Mor SK, Armien AG, Batts W, Goodwin AE, et al. (2014) Isolation and Molecular Characterization of a Novel Picornavirus from Baitfish in the USA. PLoS One 9: e87593.
    • (2014) PLoS One , vol.9 , pp. e87593
    • Phelps, N.B.D.1    Mor, S.K.2    Armien, A.G.3    Batts, W.4    Goodwin, A.E.5
  • 37
    • 84901980050 scopus 로고    scopus 로고
    • Complete genome sequence of a novel monopartite begomovirus infecting sweet potato in China
    • Liu Q, Zhang Z, Li Z, Qiao Qi, Qin Y, et al (2014) Complete genome sequence of a novel monopartite begomovirus infecting sweet potato in China. Arch Virol. DOI 10.1007/s00705-013-1958-2.
    • (2014) Arch Virol
    • Liu, Q.1    Zhang, Z.2    Li, Z.3    Qiao, Qi.4    Qin, Y.5
  • 38
  • 39
    • 84906075844 scopus 로고    scopus 로고
    • Molecular variability of Apple chlorotic leaf spot virus in Shaanxi, China
    • Liu P, Li Z, Song S, Wu Y, (2014) Molecular variability of Apple chlorotic leaf spot virus in Shaanxi, China. Arch Virol. DOI 10.1007/s12600-013-0381-2.
    • (2014) Arch Virol
    • Liu, P.1    Li, Z.2    Song, S.3    Wu, Y.4
  • 40
    • 84883775423 scopus 로고    scopus 로고
    • Identification and characterisation of a highly divergent geminivirus: Evolutionary and taxonomic implications
    • Bernardo P, Golden M, Akram M, Naimuddin, Nadarajan N, et al. (2013) Identification and characterisation of a highly divergent geminivirus: evolutionary and taxonomic implications. Virus Res 177: 35-45.
    • (2013) Virus Res , vol.177 , pp. 35-45
    • Bernardo, P.1    Golden, M.2    Akram, M.3    Naimuddin4    Nadarajan, N.5
  • 41
    • 84875233034 scopus 로고    scopus 로고
    • Avihepadnavirus diversity in parrots is comparable to that found amongst all other avian species
    • Piasecki T, Harkins GW, Chrza¸stek K, Julian L, Martin DP, et al. (2013) Avihepadnavirus diversity in parrots is comparable to that found amongst all other avian species. Virology 438: 98-105.
    • (2013) Virology , vol.438 , pp. 98-105
    • Piasecki, T.1    Harkins, G.W.2    Chrza¸stek, K.3    Julian, L.4    Martin, D.P.5
  • 42
    • 84901975965 scopus 로고    scopus 로고
    • Identification and molecular characterization of a single-stranded circular DNA virus with similarities to Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1
    • Du Z, Tang Y, Zhang S, She X, Lan G, et al. (2013) Identification and molecular characterization of a single-stranded circular DNA virus with similarities to Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1. Arch Virol. 159: 1527-1531.
    • (2013) Arch Virol , vol.159 , pp. 1527-1531
    • Du, Z.1    Tang, Y.2    Zhang, S.3    She, X.4    Lan, G.5
  • 43
    • 84893704521 scopus 로고    scopus 로고
    • Novel circular DNA viruses identified in Procordulia grayi and Xanthocnemis zealandica larvae using metagenomic approaches
    • Dayaram A, Galatowitsch M, Harding JS, Argüello-Astorga GR, Varsani A (2014) Novel circular DNA viruses identified in Procordulia grayi and Xanthocnemis zealandica larvae using metagenomic approaches. Infect Genet Evol 22: 134-141.
    • (2014) Infect Genet Evol , vol.22 , pp. 134-141
    • Dayaram, A.1    Galatowitsch, M.2    Harding, J.S.3    Argüello-Astorga, G.R.4    Varsani, A.5
  • 44
    • 84900844547 scopus 로고    scopus 로고
    • A novel papillomavirus in Adelie penguin (Pygoscelis adeliae) faeces sampled at the Cape Crozier colony, Antarctica
    • Varsani A, Kraberger S, Jennings S, Porzig EL, Julian L, et al. (2014) A novel papillomavirus in Adelie penguin (Pygoscelis adeliae) faeces sampled at the Cape Crozier colony, Antarctica. J Gen Virol. 95: 1352-1365.
    • (2014) J Gen Virol , vol.95 , pp. 1352-1365
    • Varsani, A.1    Kraberger, S.2    Jennings, S.3    Porzig, E.L.4    Julian, L.5
  • 45
    • 84902006019 scopus 로고    scopus 로고
    • Diverse small circular single-stranded DNA viruses identified in a freshwater pond on the McMurdo Ice Shelf (Antarctica)
    • Zawar-Reza P, Argüello-Astorga GR, Kraberger S, Julian L, Stainton D, et al. (2014) Diverse small circular single-stranded DNA viruses identified in a freshwater pond on the McMurdo Ice Shelf (Antarctica). Infect Genet Evol 26: 132-138.
    • (2014) Infect Genet Evol , vol.26 , pp. 132-138
    • Zawar-Reza, P.1    Argüello-Astorga, G.R.2    Kraberger, S.3    Julian, L.4    Stainton, D.5
  • 46
    • 84893474747 scopus 로고    scopus 로고
    • Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses
    • Muhire BM, Golden M, Murrell B, Lefeuvre P, Lett J, et al. (2014) Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses. J Virol 88: 1972-1989.
    • (2014) J Virol , vol.88 , pp. 1972-1989
    • Muhire, B.M.1    Golden, M.2    Murrell, B.3    Lefeuvre, P.4    Lett, J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.