메뉴 건너뛰기
Journal of Virology
Volumn 89, Issue 3, 2015, Pages 1489-1501
Unraveling the web of viroinformatics: Computational tools and databases in virus research
Author keywords

[No Author keywords available]
Indexed keywords

MICRORNA; SHORT HAIRPIN RNA; SMALL INTERFERING RNA;
EID: 84921512410     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.02027-14     Document Type: Short Survey
Times cited : (61)
References (116)
  • 4
    • 34547599217 scopus 로고    scopus 로고
    • FLAN: a web server for influenza virus genome annotation
    • Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Tatusova T. 2007. FLAN: a web server for influenza virus genome annotation. Nucleic Acids Res 35:W280-W284. http://dx.doi.org/10.1093/nar/gkm354.
    • (2007) Nucleic Acids Res , vol.35 , pp. W280-W284
    • Bao, Y.1    Bolotov, P.2    Dernovoy, D.3    Kiryutin, B.4    Tatusova, T.5
  • 5
    • 44849127354 scopus 로고    scopus 로고
    • Visualization of large influenza virus sequence datasets using adaptively aggregated trees with samplingbased subscale representation
    • Zaslavsky L, Bao Y, Tatusova TA. 2008. Visualization of large influenza virus sequence datasets using adaptively aggregated trees with samplingbased subscale representation. BMC Bioinformatics 9:237. http://dx.doi.org/10.1186/1471-2105-9-237.
    • (2008) BMC Bioinformatics , vol.9 , pp. 237
    • Zaslavsky, L.1    Bao, Y.2    Tatusova, T.A.3
  • 7
    • 33748304279 scopus 로고    scopus 로고
    • A global initiative on sharing avian flu data
    • Bogner P, Capua I, Cox NJ, Lipman DJ. 2006. A global initiative on sharing avian flu data. Nature 442:981. http://dx.doi.org/10.1038/442981a.
    • (2006) Nature , vol.442 , pp. 981
    • Bogner, P.1    Capua, I.2    Cox, N.J.3    Lipman, D.J.4
  • 8
    • 34547558387 scopus 로고    scopus 로고
    • FluGenome: a web tool for genotyping influenza A virus
    • Lu G, Rowley T, Garten R, Donis RO. 2007. FluGenome: a web tool for genotyping influenza A virus. Nucleic Acids Res 35:W275-W279. http://dx.doi.org/10.1093/nar/gkm365.
    • (2007) Nucleic Acids Res , vol.35 , pp. W275-W279
    • Lu, G.1    Rowley, T.2    Garten, R.3    Donis, R.O.4
  • 9
    • 79953677207 scopus 로고    scopus 로고
    • GiRaF: robust, computational identification of influenza reassortments via graph mining
    • Nagarajan N, Kingsford C. 2011. GiRaF: robust, computational identification of influenza reassortments via graph mining. Nucleic Acids Res 39:e34. http://dx.doi.org/10.1093/nar/gkq1232.
    • (2011) Nucleic Acids Res , vol.39
    • Nagarajan, N.1    Kingsford, C.2
  • 11
    • 67849085000 scopus 로고    scopus 로고
    • ATIVS: analytical tool for influenza virus surveillance
    • Liao YC, Ko CY, Tsai MH, Lee MS, Hsiung CA. 2009. ATIVS: analytical tool for influenza virus surveillance. Nucleic Acids Res 37:W643-W646. http://dx.doi.org/10.1093/nar/gkp321.
    • (2009) Nucleic Acids Res , vol.37 , pp. W643-W646
    • Liao, Y.C.1    Ko, C.Y.2    Tsai, M.H.3    Lee, M.S.4    Hsiung, C.A.5
  • 13
    • 65249138755 scopus 로고    scopus 로고
    • The Influenza Primer Design Resource: a new tool for translating influenza sequence data into effective diagnostics
    • Bose ME, Littrell JC, Patzer AD, Kraft AJ, Metallo JA, Fan J, Henrickson KJ. 2008. The Influenza Primer Design Resource: a new tool for translating influenza sequence data into effective diagnostics. Influenza Other Respir Viruses 2:23-31. http://dx.doi.org/10.1111/j.1750-2659.2007.00031.x.
    • (2008) Influenza Other Respir Viruses , vol.2 , pp. 23-31
    • Bose, M.E.1    Littrell, J.C.2    Patzer, A.D.3    Kraft, A.J.4    Metallo, J.A.5    Fan, J.6    Henrickson, K.J.7
  • 14
    • 76749154557 scopus 로고    scopus 로고
    • FluTE, a publicly available stochastic influenza epidemic simulation model
    • Chao DL, Halloran ME, Obenchain VJ, Longini IM, Jr. 2010. FluTE, a publicly available stochastic influenza epidemic simulation model. PLoS Comput Biol 6:e1000656. http://dx.doi.org/10.1371/journal.pcbi.1000656.
    • (2010) PLoS Comput Biol , vol.6
    • Chao, D.L.1    Halloran, M.E.2    Obenchain, V.J.3    Longini, I.M.4
  • 17
    • 84883564823 scopus 로고    scopus 로고
    • HIV N-linked glycosylation site analyzer and its further usage in anchored alignment
    • Shaw TI, Zhang M. 2013. HIV N-linked glycosylation site analyzer and its further usage in anchored alignment. Nucleic Acids Res 41:W454-W458. http://dx.doi.org/10.1093/nar/gkt472.
    • (2013) Nucleic Acids Res , vol.41 , pp. W454-W458
    • Shaw, T.I.1    Zhang, M.2
  • 18
    • 33748879209 scopus 로고    scopus 로고
    • Rationale and uses of a public HIV drug-resistance database
    • Shafer RW. 2006. Rationale and uses of a public HIV drug-resistance database. J Infect Dis 194(Suppl 1):S51-S58. http://dx.doi.org/10.1086/505356.
    • (2006) J Infect Dis , vol.194 , pp. S51-S58
    • Shafer, R.W.1
  • 20
    • 16244398637 scopus 로고    scopus 로고
    • PIRSpred: a web server for reliable HIV-1 protein-inhibitor resistance/susceptibility prediction
    • Jenwitheesuk E, Wang K, Mittler JE, Samudrala R. 2005. PIRSpred: a web server for reliable HIV-1 protein-inhibitor resistance/susceptibility prediction. Trends Microbiol 13:150-151. http://dx.doi.org/10.1016/j.tim.2005.02.003.
    • (2005) Trends Microbiol , vol.13 , pp. 150-151
    • Jenwitheesuk, E.1    Wang, K.2    Mittler, J.E.3    Samudrala, R.4
  • 21
    • 80054888112 scopus 로고    scopus 로고
    • HIV Therapy Simulator: a graphical user interface for comparing the effectiveness of novel therapy regimens
    • Lim HC, Curlin ME, Mittler JE. 2011. HIV Therapy Simulator: a graphical user interface for comparing the effectiveness of novel therapy regimens. Bioinformatics 27:3065-3066. http://dx.doi.org/10.1093/bioinformatics/btr515.
    • (2011) Bioinformatics , vol.27 , pp. 3065-3066
    • Lim, H.C.1    Curlin, M.E.2    Mittler, J.E.3
  • 23
    • 33846054821 scopus 로고    scopus 로고
    • The HIV positive selection mutation database
    • Pan C, Kim J, Chen L, Wang Q, Lee C. 2007. The HIV positive selection mutation database. Nucleic Acids Res 35:D371-D375. http://dx.doi.org/10.1093/nar/gkl855.
    • (2007) Nucleic Acids Res , vol.35 , pp. D371-D375
    • Pan, C.1    Kim, J.2    Chen, L.3    Wang, Q.4    Lee, C.5
  • 24
    • 84864248957 scopus 로고    scopus 로고
    • Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase
    • Delong AK, Wu M, Bennett D, Parkin N, Wu Z, Hogan JW, Kantor R. 2012. Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase. AIDS ResHumRetroviruses 28:894-901. http://dx.doi.org/10.1089/aid.2011.0120.
    • (2012) AIDS ResHumRetroviruses , vol.28 , pp. 894-901
    • Delong, A.K.1    Wu, M.2    Bennett, D.3    Parkin, N.4    Wu, Z.5    Hogan, J.W.6    Kantor, R.7
  • 25
    • 84891445965 scopus 로고    scopus 로고
    • Application of a new informatics tool for contamination screening in the HIV sequencing laboratory
    • Ebbert MT, Mallory MA, Wilson AR, Dooley SK, Hillyard DR. 2013. Application of a new informatics tool for contamination screening in the HIV sequencing laboratory. J Clin Virol 57:249-253. http://dx.doi.org/10.1016/j.jcv.2013.03.013.
    • (2013) J Clin Virol , vol.57 , pp. 249-253
    • Ebbert, M.T.1    Mallory, M.A.2    Wilson, A.R.3    Dooley, S.K.4    Hillyard, D.R.5
  • 27
    • 77952261538 scopus 로고    scopus 로고
    • vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments
    • Ma J, Dykes C, Wu T, Huang Y, Demeter L, Wu H. 2010. vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments. BMC Bioinformatics 11:261. http://dx.doi.org/10.1186/1471-2105-11-261.
    • (2010) BMC Bioinformatics , vol.11 , pp. 261
    • Ma, J.1    Dykes, C.2    Wu, T.3    Huang, Y.4    Demeter, L.5    Wu, H.6
  • 30
    • 65149087854 scopus 로고    scopus 로고
    • Virus variation resources at the National Center for Biotechnology Information: dengue virus
    • Resch W, Zaslavsky L, Kiryutin B, Rozanov M, Bao Y, Tatusova TA. 2009. Virus variation resources at the National Center for Biotechnology Information: dengue virus. BMC Microbiol 9:65. http://dx.doi.org/10.1186/1471-2180-9-65.
    • (2009) BMC Microbiol , vol.9 , pp. 65
    • Resch, W.1    Zaslavsky, L.2    Kiryutin, B.3    Rozanov, M.4    Bao, Y.5    Tatusova, T.A.6
  • 31
    • 0037031748 scopus 로고    scopus 로고
    • DengueNet-WHO's Internet-based system for the global surveillance of dengue fever and dengue haemorrhagic fever (dengue/DHF) http://www.who.int/denguenet. Dengue/DHF-global public health burden
    • World Health Organization. 2002. DengueNet-WHO's Internet-based system for the global surveillance of dengue fever and dengue haemorrhagic fever (dengue/DHF) http://www.who.int/denguenet. Dengue/DHF-global public health burden. Wkly Epidemiol Rec. 77:300-304.
    • (2002) Wkly Epidemiol Rec. , vol.77 , pp. 300-304
  • 32
    • 33846052599 scopus 로고    scopus 로고
    • HepSEQ: international public health repository for hepatitis B
    • Gnaneshan S, Ijaz S, Moran J, Ramsay M, Green J. 2007. HepSEQ: international public health repository for hepatitis B. Nucleic Acids Res 35:D367-D370. http://dx.doi.org/10.1093/nar/gkl874.
    • (2007) Nucleic Acids Res , vol.35 , pp. D367-D370
    • Gnaneshan, S.1    Ijaz, S.2    Moran, J.3    Ramsay, M.4    Green, J.5
  • 35
    • 38949100479 scopus 로고    scopus 로고
    • HBVRegDB: annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences
    • Panjaworayan N, Roessner SK, Firth AE, Brown CM. 2007. HBVRegDB: annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences. Virol J 4:136. http://dx.doi.org/10.1186/1743-422X-4-136.
    • (2007) Virol J , vol.4 , pp. 136
    • Panjaworayan, N.1    Roessner, S.K.2    Firth, A.E.3    Brown, C.M.4
  • 36
    • 13844253602 scopus 로고    scopus 로고
    • The Los Alamos hepatitis C sequence database
    • Kuiken C, Yusim K, Boykin L, Richardson R. 2005. The Los Alamos hepatitis C sequence database. Bioinformatics 21:379-384. http://dx.doi.org/10.1093/bioinformatics/bth485.
    • (2005) Bioinformatics , vol.21 , pp. 379-384
    • Kuiken, C.1    Yusim, K.2    Boykin, L.3    Richardson, R.4
  • 40
    • 13444283827 scopus 로고    scopus 로고
    • Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource
    • Lefkowitz EJ, Upton C, Changayil SS, Buck C, Traktman P, Buller RM. 2005. Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource. Nucleic Acids Res 33(Database issue):D311-D316. http://dx.doi.org/10.1093/nar/gki110.
    • (2005) Nucleic Acids Res , vol.33 , Issue.Database Issue , pp. D311-D316
    • Lefkowitz, E.J.1    Upton, C.2    Changayil, S.S.3    Buck, C.4    Traktman, P.5    Buller, R.M.6
  • 41
    • 0033916184 scopus 로고    scopus 로고
    • Viral Genome DataBase: storing and analyzing genes and proteins from complete viral genomes
    • Hiscock D, Upton C. 2000. Viral Genome DataBase: storing and analyzing genes and proteins from complete viral genomes. Bioinformatics 16:484-485. http://dx.doi.org/10.1093/bioinformatics/16.5.484.
    • (2000) Bioinformatics , vol.16 , pp. 484-485
    • Hiscock, D.1    Upton, C.2
  • 44
    • 84862163857 scopus 로고    scopus 로고
    • The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses
    • Kuiken C, Thurmond J, Dimitrijevic M, Yoon H. 2012. The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses. Nucleic Acids Res 40:D587-D592. http://dx.doi.org/10.1093/nar/gkr898.
    • (2012) Nucleic Acids Res , vol.40 , pp. D587-D592
    • Kuiken, C.1    Thurmond, J.2    Dimitrijevic, M.3    Yoon, H.4
  • 45
    • 35748946924 scopus 로고    scopus 로고
    • Flavitrack: an annotated database of flavivirus sequences
    • Misra M, Schein CH. 2007. Flavitrack: an annotated database of flavivirus sequences. Bioinformatics 23:2645-2647. http://dx.doi.org/10.1093/bioinformatics/btm383.
    • (2007) Bioinformatics , vol.23 , pp. 2645-2647
    • Misra, M.1    Schein, C.H.2
  • 46
    • 84866977551 scopus 로고    scopus 로고
    • FLAVIdB: a data mining system for knowledge discovery in flaviviruses with direct applications in immunology and vaccinology
    • Olsen LR, Zhang GL, Reinherz EL, Brusic V. 2011. FLAVIdB: a data mining system for knowledge discovery in flaviviruses with direct applications in immunology and vaccinology. Immunome Res 30:1-9.
    • (2011) Immunome Res , vol.30 , pp. 1-9
    • Olsen, L.R.1    Zhang, G.L.2    Reinherz, E.L.3    Brusic, V.4
  • 47
    • 38849113798 scopus 로고    scopus 로고
    • Development and public release of a comprehensive hepatitis virus database
    • Shin IT, Tanaka Y, Tateno Y, Mizokami M. 2008. Development and public release of a comprehensive hepatitis virus database. Hepatol Res 38:234-243. http://dx.doi.org/10.1111/j.1872-034X.2007.00262.x.
    • (2008) Hepatol Res , vol.38 , pp. 234-243
    • Shin, I.T.1    Tanaka, Y.2    Tateno, Y.3    Mizokami, M.4
  • 48
    • 0035171076 scopus 로고    scopus 로고
    • VIDA: a virus database system for the organization of animal virus genome open reading frames
    • Albà MM, Lee D, Pearl FM, Shepherd AJ, Martin N, Orengo CA, Kellam P. 2001. VIDA: a virus database system for the organization of animal virus genome open reading frames. Nucleic Acids Res 29:133-136. http://dx.doi.org/10.1093/nar/29.1.133.
    • (2001) Nucleic Acids Res , vol.29 , pp. 133-136
    • Albà, M.M.1    Lee, D.2    Pearl, F.M.3    Shepherd, A.J.4    Martin, N.5    Orengo, C.A.6    Kellam, P.7
  • 49
    • 31344445697 scopus 로고    scopus 로고
    • DPVweb: a comprehensive database of plant and fungal virus genes and genomes
    • Adams MJ, Antoniw JF. 2006. DPVweb: a comprehensive database of plant and fungal virus genes and genomes. Nucleic Acids Res 34:D382-D385. http://dx.doi.org/10.1093/nar/gkj023.
    • (2006) Nucleic Acids Res , vol.34 , pp. D382-D385
    • Adams, M.J.1    Antoniw, J.F.2
  • 51
    • 33645376746 scopus 로고    scopus 로고
    • The Subviral RNA Database: a toolbox for viroids, the hepatitis delta virus and satellite RNAs research
    • Rocheleau L, Pelchat M. 2006. The Subviral RNA Database: a toolbox for viroids, the hepatitis delta virus and satellite RNAs research. BMC Microbiol 6:24. http://dx.doi.org/10.1186/1471-2180-6-24.
    • (2006) BMC Microbiol , vol.6 , pp. 24
    • Rocheleau, L.1    Pelchat, M.2
  • 52
    • 75549089583 scopus 로고    scopus 로고
    • phiSITE: database of gene regulation in bacteriophages
    • Klucar L, Stano M, Hajduk M. 2010. phiSITE: database of gene regulation in bacteriophages. Nucleic Acids Res 38:D366-D370. http://dx.doi.org/10.1093/nar/gkp911.
    • (2010) Nucleic Acids Res , vol.38 , pp. D366-D370
    • Klucar, L.1    Stano, M.2    Hajduk, M.3
  • 53
    • 17444382734 scopus 로고    scopus 로고
    • HESAS: HERVs expression and structure analysis system
    • Kim TH, Jeon YJ, Kim WY, Kim HS. 2005. HESAS: HERVs expression and structure analysis system. Bioinformatics 21:1699-1700. http://dx.doi.org/10.1093/bioinformatics/bti194.
    • (2005) Bioinformatics , vol.21 , pp. 1699-1700
    • Kim, T.H.1    Jeon, Y.J.2    Kim, W.Y.3    Kim, H.S.4
  • 54
    • 0036088127 scopus 로고    scopus 로고
    • HERVd: database of human endogenous retroviruses
    • Paces J, Pavlicek A, Paces V. 2002. HERVd: database of human endogenous retroviruses. Nucleic Acids Res 30:205-206. http://dx.doi.org/10.1093/nar/30.1.205.
    • (2002) Nucleic Acids Res , vol.30 , pp. 205-206
    • Paces, J.1    Pavlicek, A.2    Paces, V.3
  • 55
    • 34548590461 scopus 로고    scopus 로고
    • Automated recognition of retroviral sequences in genomic data - RetroTector
    • Sperber GO, Airola T, Jern P, Blomberg J. 2007. Automated recognition of retroviral sequences in genomic data - RetroTector. Nucleic Acids Res 35:4964-4976. http://dx.doi.org/10.1093/nar/gkm515.
    • (2007) Nucleic Acids Res , vol.35 , pp. 4964-4976
    • Sperber, G.O.1    Airola, T.2    Jern, P.3    Blomberg, J.4
  • 56
    • 13244260787 scopus 로고    scopus 로고
    • Base-By-Base: single nucleotide-level analysis of whole viral genome alignments
    • Brodie R, Smith AJ, Roper RL, Tcherepanov V, Upton C. 2004. Base-By-Base: single nucleotide-level analysis of whole viral genome alignments. BMC Bioinformatics 5:96. http://dx.doi.org/10.1186/1471-2105-5-96.
    • (2004) BMC Bioinformatics , vol.5 , pp. 96
    • Brodie, R.1    Smith, A.J.2    Roper, R.L.3    Tcherepanov, V.4    Upton, C.5
  • 57
    • 33846033843 scopus 로고    scopus 로고
    • Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes
    • Hirahata M, Abe T, Tanaka N, Kuwana Y, Shigemoto Y, Miyazaki S, Suzuki Y, Sugawara H. 2007. Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes. Nucleic Acids Res 35:D339-D342. http://dx.doi.org/10.1093/nar/gkl1004.
    • (2007) Nucleic Acids Res , vol.35 , pp. D339-D342
    • Hirahata, M.1    Abe, T.2    Tanaka, N.3    Kuwana, Y.4    Shigemoto, Y.5    Miyazaki, S.6    Suzuki, Y.7    Sugawara, H.8
  • 58
    • 34548751162 scopus 로고    scopus 로고
    • Viro-BLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets
    • Deng W, Nickle DC, Learn GH, Maust B, Mullins JI. 2007. Viro-BLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets. Bioinformatics 23:2334-2336. http://dx.doi.org/10.1093/bioinformatics/btm331.
    • (2007) Bioinformatics , vol.23 , pp. 2334-2336
    • Deng, W.1    Nickle, D.C.2    Learn, G.H.3    Maust, B.4    Mullins, J.I.5
  • 59
    • 34548580467 scopus 로고    scopus 로고
    • Alvira: comparative genomics of viral strains
    • Enault F, Fremez R, Baranowski E, Faraut T. 2007. Alvira: comparative genomics of viral strains. Bioinformatics 23:2178-2179. http://dx.doi.org/10.1093/bioinformatics/btm293.
    • (2007) Bioinformatics , vol.23 , pp. 2178-2179
    • Enault, F.1    Fremez, R.2    Baranowski, E.3    Faraut, T.4
  • 60
    • 38549130737 scopus 로고    scopus 로고
    • CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes
    • Huang Y, Lau SK, Woo PC, Yuen KY. 2008. CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes. Nucleic Acids Res36(Database issue):D504-D511. http://dx.doi.org/10.1093/nar/gkm754.
    • (2008) Nucleic Acids Res , vol.36 , Issue.Database Issue , pp. D504-D511
    • Huang, Y.1    Lau, S.K.2    Woo, P.C.3    Yuen, K.Y.4
  • 62
    • 84856017600 scopus 로고    scopus 로고
    • SSE: a nucleotide and amino acid sequence analysis platform
    • Simmonds P. 2012. SSE: a nucleotide and amino acid sequence analysis platform. BMC Res Notes 5:50. http://dx.doi.org/10.1186/1756-0500-5-50.
    • (2012) BMC Res Notes , vol.5 , pp. 50
    • Simmonds, P.1
  • 64
    • 78651460018 scopus 로고    scopus 로고
    • PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes
    • Yu Q, Ryan EM, Allen TM, Birren BW, Henn MR, Lennon NJ. 2011. PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes. Bioinformatics 27:266-267. http://dx.doi.org/10.1093/bioinformatics/btq624.
    • (2011) Bioinformatics , vol.27 , pp. 266-267
    • Yu, Q.1    Ryan, E.M.2    Allen, T.M.3    Birren, B.W.4    Henn, M.R.5    Lennon, N.J.6
  • 67
    • 80053379379 scopus 로고    scopus 로고
    • TheViral MetaGenome Annotation Pipeline (VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data
    • Lorenzi HA, Hoover J, Inman J, Safford T, Murphy S, Kagan L, Williamson SJ. 2011. TheViral MetaGenome Annotation Pipeline (VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data. Stand Genomic Sci 4:418-429. http://dx.doi.org/10.4056/sigs.1694706.
    • (2011) Stand Genomic Sci , vol.4 , pp. 418-429
    • Lorenzi, H.A.1    Hoover, J.2    Inman, J.3    Safford, T.4    Murphy, S.5    Kagan, L.6    Williamson, S.J.7
  • 71
    • 84893239082 scopus 로고    scopus 로고
    • Discovery of functional genomic motifs in viruses with ViReMa-a virus Recombination Mapper-for analysis of next-generation sequencing data
    • Routh A, Johnson JE. 2014. Discovery of functional genomic motifs in viruses with ViReMa-a virus Recombination Mapper-for analysis of next-generation sequencing data. Nucleic Acids Res 42:e11. http://dx.doi.org/10.1093/nar/gkt916.
    • (2014) Nucleic Acids Res , vol.42
    • Routh, A.1    Johnson, J.E.2
  • 72
    • 84869452410 scopus 로고    scopus 로고
    • VIPR HMM:a hidden Markov model for detecting recombination with microbial detection microarrays
    • Allred AF, Renshaw H, Weaver S, Tesh RB, Wang D. 2012. VIPR HMM:a hidden Markov model for detecting recombination with microbial detection microarrays. Bioinformatics 28:2922-2929. http://dx.doi.org/10.1093/bioinformatics/bts560.
    • (2012) Bioinformatics , vol.28 , pp. 2922-2929
    • Allred, A.F.1    Renshaw, H.2    Weaver, S.3    Tesh, R.B.4    Wang, D.5
  • 73
    • 77954265331 scopus 로고    scopus 로고
    • SeLOX-a locus of recombination site search tool for the detection and directed evolution of site-specific recombination systems
    • Surendranath V, Chusainow J, Hauber J, Buchholz F, Habermann BH. 2010. SeLOX-a locus of recombination site search tool for the detection and directed evolution of site-specific recombination systems. Nucleic Acids Res 38:W293-W298. http://dx.doi.org/10.1093/nar/gkq523.
    • (2010) Nucleic Acids Res , vol.38 , pp. W293-W298
    • Surendranath, V.1    Chusainow, J.2    Hauber, J.3    Buchholz, F.4    Habermann, B.H.5
  • 74
    • 84894549844 scopus 로고    scopus 로고
    • VIRAPOPS: a forward simulator dedicated to rapidly evolved viral populations
    • Petitjean M, Vanet A. 2014. VIRAPOPS: a forward simulator dedicated to rapidly evolved viral populations. Bioinformatics 30:578-580. http://dx.doi.org/10.1093/bioinformatics/btt724.
    • (2014) Bioinformatics , vol.30 , pp. 578-580
    • Petitjean, M.1    Vanet, A.2
  • 76
    • 84874720727 scopus 로고    scopus 로고
    • ViralFusion-Seq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution
    • Li JW, Wan R, Yu CS, Co NN, Wong N, Chan TF. 2013. ViralFusion-Seq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution. Bioinformatics 29:649-651. http://dx.doi.org/10.1093/bioinformatics/btt011.
    • (2013) Bioinformatics , vol.29 , pp. 649-651
    • Li, J.W.1    Wan, R.2    Yu, C.S.3    Co, N.N.4    Wong, N.5    Chan, T.F.6
  • 77
    • 84872583615 scopus 로고    scopus 로고
    • VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue
    • Chen Y, Yao H, Thompson EJ, Tannir NM, Weinstein JN, Su X. 2013. VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue. Bioinformatics 29:266-267. http://dx.doi.org/10.1093/bioinformatics/bts665.
    • (2013) Bioinformatics , vol.29 , pp. 266-267
    • Chen, Y.1    Yao, H.2    Thompson, E.J.3    Tannir, N.M.4    Weinstein, J.N.5    Su, X.6
  • 78
    • 84878151016 scopus 로고    scopus 로고
    • VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data
    • Wang Q, Jia P, 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. http://dx.doi.org/10.1371/journal.pone.0064465.
    • (2013) PLoS One , vol.8
    • Wang, Q.1    Jia, P.2    Zhao, Z.3
  • 79
    • 84860113335 scopus 로고    scopus 로고
    • Dr.VIS: a database of human disease-related viral integration sites
    • Zhao X, Liu Q, Cai Q, Li Y, Xu C, Li Z, Zhang X. 2012. Dr.VIS: a database of human disease-related viral integration sites. Nucleic Acids Res 40:D1041-D1046. http://dx.doi.org/10.1093/nar/gkr1142.
    • (2012) Nucleic Acids Res , vol.40 , pp. D1041-D1046
    • Zhao, X.1    Liu, Q.2    Cai, Q.3    Li, Y.4    Xu, C.5    Li, Z.6    Zhang, X.7
  • 80
    • 33846033396 scopus 로고    scopus 로고
    • ViTa: prediction of host microRNAs targets on viruses
    • Hsu PW, Lin LZ, Hsu SD, Hsu JB, Huang HD. 2007. ViTa: prediction of host microRNAs targets on viruses. Nucleic Acids Res 35:D381-D385. http://dx.doi.org/10.1093/nar/gkl1009.
    • (2007) Nucleic Acids Res , vol.35 , pp. D381-D385
    • Hsu, P.W.1    Lin, L.Z.2    Hsu, S.D.3    Hsu, J.B.4    Huang, H.D.5
  • 81
    • 38549083644 scopus 로고    scopus 로고
    • Vir-Mir db: prediction of viral microRNA candidate hairpins
    • Li SC, Shiau CK, Lin WC. 2008. Vir-Mir db: prediction of viral microRNA candidate hairpins. Nucleic Acids Res 36:D184-D189. http://dx.doi.org/10.1093/nar/gkm610.
    • (2008) Nucleic Acids Res , vol.36 , pp. D184-D189
    • Li, S.C.1    Shiau, C.K.2    Lin, W.C.3
  • 83
    • 84862160087 scopus 로고    scopus 로고
    • VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA
    • Thakur N, Qureshi A, Kumar M. 2012. VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA. Nucleic Acids Res 40:D230-D236. http://dx.doi.org/10.1093/nar/gkr1147.
    • (2012) Nucleic Acids Res , vol.40 , pp. D230-D236
    • Thakur, N.1    Qureshi, A.2    Kumar, M.3
  • 84
    • 33747869038 scopus 로고    scopus 로고
    • siVirus: web-based antiviral siRNA design software for highly divergent viral sequences
    • Naito Y, Ui-Tei K, Nishikawa T, Takebe Y, Saigo K. 2006. siVirus: web-based antiviral siRNA design software for highly divergent viral sequences. Nucleic Acids Res 34:W448-W450. http://dx.doi.org/10.1093/nar/gkl214.
    • (2006) Nucleic Acids Res , vol.34 , pp. W448-W450
    • Naito, Y.1    Ui-Tei, K.2    Nishikawa, T.3    Takebe, Y.4    Saigo, K.5
  • 85
    • 84889766420 scopus 로고    scopus 로고
    • VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses
    • Qureshi A, Thakur N, Kumar M. 2013. VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses. J Transl Med 11:305. http://dx.doi.org/10.1186/1479-5876-11-305.
    • (2013) J Transl Med , vol.11 , pp. 305
    • Qureshi, A.1    Thakur, N.2    Kumar, M.3
  • 86
    • 79960046911 scopus 로고    scopus 로고
    • Visitor, an informatic pipeline for analysis of viral siRNA sequencing datasets
    • Antoniewski C. 2011. Visitor, an informatic pipeline for analysis of viral siRNA sequencing datasets. Methods Mol Biol 721:123-142. http://dx.doi.org/10.1007/978-1-61779-037-9_7.
    • (2011) Methods Mol Biol , vol.721 , pp. 123-142
    • Antoniewski, C.1
  • 87
    • 84880547557 scopus 로고    scopus 로고
    • viRome: an R package for the visualization and analysis of viral small RNA sequence datasets
    • Watson M, Schnettler E, Kohl A. 2013. viRome: an R package for the visualization and analysis of viral small RNA sequence datasets. Bioinformatics 29:1902-1903. http://dx.doi.org/10.1093/bioinformatics/btt297.
    • (2013) Bioinformatics , vol.29 , pp. 1902-1903
    • Watson, M.1    Schnettler, E.2    Kohl, A.3
  • 88
    • 80055104802 scopus 로고    scopus 로고
    • In silico reconstruction of viral genomes from small RNAs improves virus-derived small interfering RNA profiling
    • Vodovar N, Goic B, Blanc H, Saleh MC. 2011. In silico reconstruction of viral genomes from small RNAs improves virus-derived small interfering RNA profiling. J Virol 85:11016-11021. http://dx.doi.org/10.1128/JVI.05647-11.
    • (2011) J Virol , vol.85 , pp. 11016-11021
    • Vodovar, N.1    Goic, B.2    Blanc, H.3    Saleh, M.C.4
  • 89
    • 17144409109 scopus 로고    scopus 로고
    • HBVPathDB: a database of HBV infection-related molecular interaction network
    • Zhang Y, Bo XC, Yang J, Wang SQ. 2005. HBVPathDB: a database of HBV infection-related molecular interaction network. World J Gastroenterol 11:1690-1692.
    • (2005) World J Gastroenterol , vol.11 , pp. 1690-1692
    • Zhang, Y.1    Bo, X.C.2    Yang, J.3    Wang, S.Q.4
  • 92
    • 58149200940 scopus 로고    scopus 로고
    • Human immunodeficiency virus type 1, human protein interaction database at NCBI
    • Fu W, Sanders-Beer BE, Katz KS, Maglott DR, Pruitt KD, Ptak RG. 2009. Human immunodeficiency virus type 1, human protein interaction database at NCBI. Nucleic Acids Res 37:D417-D422. http://dx.doi.org/10.1093/nar/gkn708.
    • (2009) Nucleic Acids Res , vol.37 , pp. D417-D422
    • Fu, W.1    Sanders-Beer, B.E.2    Katz, K.S.3    Maglott, D.R.4    Pruitt, K.D.5    Ptak, R.G.6
  • 93
    • 70349116906 scopus 로고    scopus 로고
    • CAPIH: a Web interface for comparative analyses and visualization of host-HIV protein-protein interactions
    • Lin FK, Pan CL, Yang JM, Chuang TJ, Chen FC. 2009. CAPIH: a Web interface for comparative analyses and visualization of host-HIV protein-protein interactions. BMC Microbiol 9:164. http://dx.doi.org/10.1186/1471-2180-9-164.
    • (2009) BMC Microbiol , vol.9 , pp. 164
    • Lin, F.K.1    Pan, C.L.2    Yang, J.M.3    Chuang, T.J.4    Chen, F.C.5
  • 94
    • 78651342484 scopus 로고    scopus 로고
    • PhEVER: a database for the global exploration of virus-host evolutionary relationships
    • Palmeira L, Penel S, Lotteau V, Rabourdin-Combe C, Gautier C. 2011. PhEVER: a database for the global exploration of virus-host evolutionary relationships. Nucleic Acids Res 39:D569-D575. http://dx.doi.org/10.1093/nar/gkq1013.
    • (2011) Nucleic Acids Res , vol.39 , pp. D569-D575
    • Palmeira, L.1    Penel, S.2    Lotteau, V.3    Rabourdin-Combe, C.4    Gautier, C.5
  • 96
    • 77956486571 scopus 로고    scopus 로고
    • VIGOR, an annotation program for small viral genomes
    • Wang S, Sundaram JP, Spiro D. 2010. VIGOR, an annotation program for small viral genomes. BMC Bioinformatics 11:451. http://dx.doi.org/10.1186/1471-2105-11-451.
    • (2010) BMC Bioinformatics , vol.11 , pp. 451
    • Wang, S.1    Sundaram, J.P.2    Spiro, D.3
  • 97
    • 0033765762 scopus 로고    scopus 로고
    • Viral genome organizer: a system for analyzing complete viral genomes
    • Upton C, Hogg D, Perrin D, Boone M, Harris NL. 2000. Viral genome organizer: a system for analyzing complete viral genomes. Virus Res 70:55-64. http://dx.doi.org/10.1016/S0168-1702(00)00210-0.
    • (2000) Virus Res , vol.70 , pp. 55-64
    • Upton, C.1    Hogg, D.2    Perrin, D.3    Boone, M.4    Harris, N.L.5
  • 98
    • 33747092661 scopus 로고    scopus 로고
    • Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome
    • Tcherepanov V, Ehlers A, Upton C. 2006. Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome. BMC Genomics 7:150. http://dx.doi.org/10.1186/1471-2164-7-150.
    • (2006) BMC Genomics , vol.7 , pp. 150
    • Tcherepanov, V.1    Ehlers, A.2    Upton, C.3
  • 100
    • 30844454225 scopus 로고    scopus 로고
    • ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes
    • Guo FB, Zhang CT. 2006. ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes. BMC Bioinformatics 7:9. http://dx.doi.org/10.1186/1471-2105-7-9.
    • (2006) BMC Bioinformatics , vol.7 , pp. 9
    • Guo, F.B.1    Zhang, C.T.2
  • 101
    • 24144500828 scopus 로고    scopus 로고
    • A statistical model for HIV-1 sequence classification using the subtype analyser (STAR)
    • Myers RE, Gale CV, Harrison A, Takeuchi Y, Kellam P. 2005. A statistical model for HIV-1 sequence classification using the subtype analyser (STAR). Bioinformatics 21:3535-3540. http://dx.doi.org/10.1093/bioinformatics/bti569.
    • (2005) Bioinformatics , vol.21 , pp. 3535-3540
    • Myers, R.E.1    Gale, C.V.2    Harrison, A.3    Takeuchi, Y.4    Kellam, P.5
  • 102
    • 84921478408 scopus 로고    scopus 로고
    • HPV-QUEST: a highly customized system for automated HPV sequence analysis capable of processing next generation sequencing data set
    • Yin L, Yao J, Gardner BP, Chang K, Yu F, Goodenow MM. 2012. HPV-QUEST: a highly customized system for automated HPV sequence analysis capable of processing next generation sequencing data set. Bioinformation 8:388-390. http://dx.doi.org/10.6026/97320630008388.
    • (2012) Bioinformation , vol.8 , pp. 388-390
    • Yin, L.1    Yao, J.2    Gardner, B.P.3    Chang, K.4    Yu, F.5    Goodenow, M.M.6
  • 104
    • 65849214907 scopus 로고    scopus 로고
    • PrimerHunter: a primer design tool for PCR-based virus subtype identification
    • Duitama J, Kumar DM, Hemphill E, Khan M, Mandoiu II, Nelson CE. 2009. PrimerHunter: a primer design tool for PCR-based virus subtype identification. Nucleic Acids Res 37:2483-2492. http://dx.doi.org/10.1093/nar/gkp073.
    • (2009) Nucleic Acids Res , vol.37 , pp. 2483-2492
    • Duitama, J.1    Kumar, D.M.2    Hemphill, E.3    Khan, M.4    Mandoiu, I.I.5    Nelson, C.E.6
  • 107
    • 72449136215 scopus 로고    scopus 로고
    • RotaC: a web-based tool for the complete genome classification of group A rotaviruses
    • Maes P, Matthijnssens J, Rahman M, Van Ranst M. 2009. RotaC: a web-based tool for the complete genome classification of group A rotaviruses. BMC Microbiol 9:238. http://dx.doi.org/10.1186/1471-2180-9-238.
    • (2009) BMC Microbiol , vol.9 , pp. 238
    • Maes, P.1    Matthijnssens, J.2    Rahman, M.3    Van Ranst, M.4
  • 108
    • 0036089478 scopus 로고    scopus 로고
    • VirOligo: a database of virus-specific oligonucleotides
    • Onodera K, Melcher U. 2002. VirOligo: a database of virus-specific oligonucleotides. Nucleic Acids Res 30:203-204. http://dx.doi.org/10.1093/nar/30.1.203.
    • (2002) Nucleic Acids Res , vol.30 , pp. 203-204
    • Onodera, K.1    Melcher, U.2
  • 109
    • 33847260136 scopus 로고    scopus 로고
    • Virus-PLoc: a fusion classifier for predicting the subcellular localization of viral proteins within host and virusinfected cells
    • Shen HB, Chou KC. 2007. Virus-PLoc: a fusion classifier for predicting the subcellular localization of viral proteins within host and virusinfected cells. Biopolymers 85:233-240. http://dx.doi.org/10.1002/bip.20640.
    • (2007) Biopolymers , vol.85 , pp. 233-240
    • Shen, H.B.1    Chou, K.C.2
  • 110
    • 84872851002 scopus 로고    scopus 로고
    • HIPdb: a database of experimentally validated HIV inhibiting peptides
    • Qureshi A, Thakur N, Kumar M. 2013. HIPdb: a database of experimentally validated HIV inhibiting peptides. PLoS One 8:e54908. http://dx.doi.org/10.1371/journal.pone.0054908.
    • (2013) PLoS One , vol.8
    • Qureshi, A.1    Thakur, N.2    Kumar, M.3
  • 111
    • 84891793411 scopus 로고    scopus 로고
    • AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses
    • Qureshi A, Thakur N, Tandon H, Kumar M. 2014. AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses. Nucleic Acids Res 42:D1147-D1153. http://dx.doi.org/10.1093/nar/gkt1191.
    • (2014) Nucleic Acids Res , vol.42 , pp. D1147-D1153
    • Qureshi, A.1    Thakur, N.2    Tandon, H.3    Kumar, M.4
  • 112
    • 84864447533 scopus 로고    scopus 로고
    • AVPpred: collection and prediction of highly effective antiviral peptides
    • Thakur N, Qureshi A, Kumar M. 2012. AVPpred: collection and prediction of highly effective antiviral peptides. Nucleic Acids Res 40: W199-W204. http://dx.doi.org/10.1093/nar/gks450.
    • (2012) Nucleic Acids Res , vol.40 , pp. W199-W204
    • Thakur, N.1    Qureshi, A.2    Kumar, M.3
  • 113
    • 84892380471 scopus 로고    scopus 로고
    • Viral IRES prediction system - a web server for prediction of the IRES secondary structure in silico
    • Hong JJ, Wu TY, Chang TY, Chen CY. 2013. Viral IRES prediction system - a web server for prediction of the IRES secondary structure in silico. PLoS One 8:e79288. http://dx.doi.org/10.1371/journal.pone.0079288.
    • (2013) PLoS One , vol.8
    • Hong, J.J.1    Wu, T.Y.2    Chang, T.Y.3    Chen, C.Y.4
  • 114
    • 14744282925 scopus 로고    scopus 로고
    • VaZyMolO: a tool to define and classify modularity in viral proteins
    • Ferron F, Rancurel C, Longhi S, Cambillau C, Henrissat B, Canard B. 2005. VaZyMolO: a tool to define and classify modularity in viral proteins. J Gen Virol 86:743-749. http://dx.doi.org/10.1099/vir.0.80590-0.
    • (2005) J Gen Virol , vol.86 , pp. 743-749
    • Ferron, F.1    Rancurel, C.2    Longhi, S.3    Cambillau, C.4    Henrissat, B.5    Canard, B.6
  • 115
    • 0033618320 scopus 로고    scopus 로고
    • LearnCoil-VMF: computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins
    • Singh M, Berger B, Kim PS. 1999. LearnCoil-VMF: computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins. J Mol Biol 290:1031-1041. http://dx.doi.org/10.1006/jmbi.1999.2796.
    • (1999) J Mol Biol , vol.290 , pp. 1031-1041
    • Singh, M.1    Berger, B.2    Kim, P.S.3

* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.