메뉴 건너뛰기




Volumn 2017, Issue , 2017, Pages

GenomeHubs: Simple containerized setup of a custom Ensembl database and web server for any species

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; DATA BASE; DNA SEQUENCE; GENOME; HUMAN; INTERNET; NUCLEIC ACID DATABASE; PROCEDURES; WEB BROWSER;

EID: 85037588099     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bax039     Document Type: Article
Times cited : (12)

References (28)
  • 1
    • 84976870063 scopus 로고    scopus 로고
    • The international nucleotide sequence database collaboration
    • and International Nucleotide Sequence Database Collaboration
    • Cochrane,G., Karsch-Mizrachi,I. and Takagi,T. and International Nucleotide Sequence Database Collaboration (2016) The international nucleotide sequence database collaboration. Nucleic Acids Res., 44, D48–D50.
    • (2016) Nucleic Acids Res , vol.44 , pp. D48-D50
    • Cochrane, G.1    Karsch-Mizrachi, I.2    Takagi, T.3
  • 2
    • 84875628769 scopus 로고    scopus 로고
    • Using GBrowse 2.0 to visualize and share next-generation sequence data
    • Stein,L.D. (2013) Using GBrowse 2.0 to visualize and share next-generation sequence data. Brief Bioinformatics, 14, 162–171.
    • (2013) Brief Bioinformatics , vol.14 , pp. 162-171
    • Stein, L.D.1
  • 3
    • 69749083447 scopus 로고    scopus 로고
    • JBrowse: a next-generation genome browser
    • Skinner,M.E., Uzilov,A.V., Stein,L.D. et al. (2009) JBrowse: a next-generation genome browser. Genome Res., 19, 1630–1638.
    • (2009) Genome Res , vol.19 , pp. 1630-1638
    • Skinner, M.E.1    Uzilov, A.V.2    Stein, L.D.3
  • 4
    • 84976878634 scopus 로고    scopus 로고
    • The UCSC Genome Browser database: 2016 update
    • Speir,M.L., Zweig,A.S., Rosenbloom,K.R. et al. (2016) The UCSC Genome Browser database: 2016 update. Nucleic Acids Res., 44, D717–D725.
    • (2016) Nucleic Acids Res , vol.44 , pp. D717-D725
    • Speir, M.L.1    Zweig, A.S.2    Rosenbloom, K.R.3
  • 5
    • 84904812243 scopus 로고    scopus 로고
    • InterMine: extensive web services for modern biology
    • Kalderimis,A., Lyne,R., Butano,D. et al. (2014) InterMine: extensive web services for modern biology. Nucleic Acids Res., 42, W468–W472.
    • (2014) Nucleic Acids Res , vol.42 , pp. W468-W472
    • Kalderimis, A.1    Lyne, R.2    Butano, D.3
  • 6
    • 84946494739 scopus 로고    scopus 로고
    • The plant genome integrative explorer resource: plantGenIE.org
    • Sundell,D., Mannapperuma,C., Netotea,S. et al. (2015) The plant genome integrative explorer resource: plantGenIE.org. New Phytol., 208, 1149–1156.
    • (2015) New Phytol , vol.208 , pp. 1149-1156
    • Sundell, D.1    Mannapperuma, C.2    Netotea, S.3
  • 8
    • 84941071987 scopus 로고    scopus 로고
    • VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases
    • Giraldo-Calderon,G.I., Emrich,S.J., MacCallum,R.M. et al. (2015) VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic Acids Res., 43, D707–D713.
    • (2015) Nucleic Acids Res , vol.43 , pp. D707-D713
    • Giraldo-Calderon, G.I.1    Emrich, S.J.2    MacCallum, R.M.3
  • 9
    • 85007451784 scopus 로고    scopus 로고
    • WormBase ParaSite - a comprehensive resource for helminth genomics
    • Howe,K.L., Bolt,B.J., Shafie,M. et al. (2016) WormBase ParaSite - a comprehensive resource for helminth genomics. Mol. Biochem. Parasitol., 10.1016/j.molbiopara.2016.11.005.
    • (2016) Mol. Biochem. Parasitol
    • Howe, K.L.1    Bolt, B.J.2    Shafie, M.3
  • 10
    • 84939205162 scopus 로고    scopus 로고
    • Avianbase: a community resource for bird genomics
    • Eöry,L., Gilbert,M.T.P., Li,C. et al. (2015) Avianbase: a community resource for bird genomics. Genome Biol., 16, 21.
    • (2015) Genome Biol , vol.16 , pp. 21
    • Eöry, L.1    Gilbert, M.T.P.2    Li, C.3
  • 11
    • 84979255809 scopus 로고    scopus 로고
    • Gramene 2016: comparative plant genomics and pathway resources
    • Tello-Ruiz,M.K., Stein,J., Wei,S. et al. (2016) Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res., 44, D1133–D1140.
    • (2016) Nucleic Acids Res , vol.44 , pp. D1133-D1140
    • Tello-Ruiz, M.K.1    Stein, J.2    Wei, S.3
  • 12
  • 13
    • 84976887033 scopus 로고    scopus 로고
    • Ensembl Genomes 2016: more genomes, more complexity
    • Kersey,P.J., Allen,J.E., Armean,I. et al. (2016) Ensembl Genomes 2016: more genomes, more complexity. Nucleic Acids Res., 44, D574–D580.
    • (2016) Nucleic Acids Res , vol.44 , pp. D574-D580
    • Kersey, P.J.1    Allen, J.E.2    Armean, I.3
  • 14
    • 84959252809 scopus 로고    scopus 로고
    • Sequenceserver: a modern graphical user interface for custom BLAST databases
    • Priyam,A., Woodcroft,B.J., Rai,V. et al. (2015) Sequenceserver: a modern graphical user interface for custom BLAST databases. bioRxiv., 10, 1101–033142.
    • (2015) bioRxiv , vol.10 , pp. 1101-033142
    • Priyam, A.1    Woodcroft, B.J.2    Rai, V.3
  • 15
    • 34249848751 scopus 로고    scopus 로고
    • CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
    • Parra,G., Bradnam,K., and Korf,I. (2007) CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics, 23, 1061–1067.
    • (2007) Bioinformatics , vol.23 , pp. 1061-1067
    • Parra, G.1    Bradnam, K.2    Korf, I.3
  • 16
    • 84940907209 scopus 로고    scopus 로고
    • BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
    • Simão,F.A., Waterhouse,R.M., Ioannidis,P. et al. (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31, 3210–3212.
    • (2015) Bioinformatics , vol.31 , pp. 3210-3212
    • Simão, F.A.1    Waterhouse, R.M.2    Ioannidis, P.3
  • 17
    • 85101737790 scopus 로고    scopus 로고
    • (–2015) RepeatMasker Open-4.0
    • Smit,A., Hubley,R., and Green,P. (2013–2015) RepeatMasker Open-4.0, http://www.repeatmasker.org.
    • (2013)
    • Smit, A.1    Hubley, R.2    Green, P.3
  • 18
    • 84946062228 scopus 로고    scopus 로고
    • UniProtKB/SwissProt, the manually annotated section of the uniprot knowledgebase: how to use the entry view
    • Boutet,E., Lieberherr,D., Tognolli,M. et al. (2016) UniProtKB/SwissProt, the manually annotated section of the uniprot knowledgebase: how to use the entry view. Methods Mol. Biol., 1374, 23–54.
    • (2016) Methods Mol. Biol , vol.1374 , pp. 23-54
    • Boutet, E.1    Lieberherr, D.2    Tognolli, M.3
  • 19
    • 84919689372 scopus 로고    scopus 로고
    • The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera
    • Ahola,V., Lehtonen,R., Somervuo,P. et al. (2014) The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera. Nat. Commun., 5, 4737.
    • (2014) Nat. Commun , vol.5 , pp. 4737
    • Ahola, V.1    Lehtonen, R.2    Somervuo, P.3
  • 20
    • 84954309315 scopus 로고    scopus 로고
    • The Genome of Winter Moth (Operophtera brumata) Provides a Genomic Perspective on Sexual Dimorphism and Phenology
    • Derks,M.F.L., Smit,S., Salis,L. et al. (2015) The Genome of Winter Moth (Operophtera brumata) Provides a Genomic Perspective on Sexual Dimorphism and Phenology. Genome Biol. Evol., 7, 2321–2332.
    • (2015) Genome Biol. Evol , vol.7 , pp. 2321-2332
    • Derks, M.F.L.1    Smit, S.2    Salis, L.3
  • 21
    • 85101765886 scopus 로고    scopus 로고
    • rjchallis/assembly-stats 17.02 [Data set]
    • Zenodo
    • Challis,R.J. (2017). rjchallis/assembly-stats 17.02 [Data set]. Zenodo. http://doi.org/10.5281/zenodo.322347
    • (2017)
    • Challis, R.J.1
  • 22
    • 85101735142 scopus 로고    scopus 로고
    • rjchallis/codon-usage 17.02 [Data set]
    • Zenodo
    • Challis,R.J. (2017). rjchallis/codon-usage 17.02 [Data set]. Zenodo. http://doi.org/10.5281/zenodo.322348.
    • (2017)
    • Challis, R.J.1
  • 23
    • 84885406698 scopus 로고    scopus 로고
    • GNU Parallel - the command-line power tool
    • login
    • Tange,O. (2011) GNU Parallel - the command-line power tool.; login: The USENIX Magazine, 36, 42–47.
    • (2011) The USENIX Magazine , vol.36 , pp. 42-47
    • Tange, O.1
  • 24
    • 85016141786 scopus 로고    scopus 로고
    • InterPro in 2017-beyond protein family and domain annotations
    • Finn,R.D., Attwood,T.K., Babbitt,P.C. et al. (2017) InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res., 45, D190–D199.
    • (2017) Nucleic Acids Res , vol.45 , pp. D190-D199
    • Finn, R.D.1    Attwood, T.K.2    Babbitt, P.C.3
  • 25
    • 84969135108 scopus 로고    scopus 로고
    • Reminder to deposit DNA sequences
    • Blaxter,M., Danchin,A., Savakis,B. et al. (2016) Reminder to deposit DNA sequences. Science, 352, 780.
    • (2016) Science , vol.352 , pp. 780
    • Blaxter, M.1    Danchin, A.2    Savakis, B.3
  • 26
    • 84976875290 scopus 로고    scopus 로고
    • WormBase 2016: expanding to enable helminth genomic research
    • Howe,K.L., Bolt,B.J., Cain,S. et al. (2016) WormBase 2016: expanding to enable helminth genomic research. Nucleic Acids Res., 44, D774–D780.
    • (2016) Nucleic Acids Res , vol.44 , pp. D774-D780
    • Howe, K.L.1    Bolt, B.J.2    Cain, S.3
  • 27
    • 85021355600 scopus 로고    scopus 로고
    • Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus
    • Yoshida,Y., Koutsovoulos,G., Laetsch,D.R. et al. (2017) Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus. bioRxiv., 10, 1101–112664.
    • (2017) bioRxiv , vol.10 , pp. 1101-112664
    • Yoshida, Y.1    Koutsovoulos, G.2    Laetsch, D.R.3
  • 28
    • 84973338712 scopus 로고    scopus 로고
    • The Ensembl Variant Effect Predictor
    • McLaren,W., Gil,L., Hunt,S.E. et al. (2016) The Ensembl Variant Effect Predictor. Genome Biol., 17,122.
    • (2016) Genome Biol , vol.17 , pp. 122
    • McLaren, W.1    Gil, L.2    Hunt, S.E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.