메뉴 건너뛰기




Volumn 44, Issue D1, 2016, Pages D286-D293

EGGNOG 4.5: A hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; ARCHAEAL PROTEIN; BACTERIAL PROTEIN; VIRAL PROTEIN;

EID: 84976905626     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1248     Document Type: Article
Times cited : (1567)

References (53)
  • 2
    • 65449142156 scopus 로고    scopus 로고
    • How confident can we be that orthologs are similar, but paralogs differ?
    • Studer, R. A. and Robinson-Rechavi, M. (2009) How confident can we be that orthologs are similar, but paralogs differ? Trends Genet., 25, 210-216.
    • (2009) Trends Genet. , vol.25 , pp. 210-216
    • Studer, R.A.1    Robinson-Rechavi, M.2
  • 3
    • 79959828326 scopus 로고    scopus 로고
    • Testing the ortholog conjecture with comparative functional genomic data from mammals
    • Nehrt, N. L., Clark, W. T., Radivojac, P. and Hahn, M. W. (2011) Testing the ortholog conjecture with comparative functional genomic data from mammals. PLoS Comput. Biol., 7, e1002073.
    • (2011) PLoS Comput. Biol. , vol.7 , pp. e1002073
    • Nehrt, N.L.1    Clark, W.T.2    Radivojac, P.3    Hahn, M.W.4
  • 4
    • 84876665869 scopus 로고    scopus 로고
    • Functional and evolutionary implications of gene orthology
    • Gabaldón, T. and Koonin, E. V. (2013) Functional and evolutionary implications of gene orthology. Nat. Rev. Genet., 14, 360-366.
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 360-366
    • Gabaldón, T.1    Koonin, E.V.2
  • 5
    • 27644472372 scopus 로고    scopus 로고
    • Orthologs, paralogs, and evolutionary genomics
    • Koonin, E. V. (2005) Orthologs, paralogs, and evolutionary genomics. Annu. Rev. Genet., 39, 309-338.
    • (2005) Annu. Rev. Genet. , vol.39 , pp. 309-338
    • Koonin, E.V.1
  • 6
    • 80052823795 scopus 로고    scopus 로고
    • Orthology prediction methods: A quality assessment using curated protein families
    • Trachana, K., Larsson, T. A., Powell, S., Chen, W.-H., Doerks, T., Muller, J. and Bork, P. (2011) Orthology prediction methods: a quality assessment using curated protein families. Bioessays, 33, 769-780.
    • (2011) Bioessays , vol.33 , pp. 769-780
    • Trachana, K.1    Larsson, T.A.2    Powell, S.3    Chen, W.-H.4    Doerks, T.5    Muller, J.6    Bork, P.7
  • 7
    • 84934300828 scopus 로고    scopus 로고
    • A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation
    • Trachana, K., Forslund, K., Larsson, T., Powell, S., Doerks, T., Mering, C. and Von Bork, P. (2014) A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. PLoS One, 9, e111122.
    • (2014) PLoS One , vol.9 , pp. e111122
    • Trachana, K.1    Forslund, K.2    Larsson, T.3    Powell, S.4    Doerks, T.5    Mering, C.6    Von Bork, P.7
  • 9
    • 33644787447 scopus 로고    scopus 로고
    • OrthoMCL-DB: Querying a comprehensive multi-species collection of ortholog groups
    • Chen, F., Mackey, A. J., Stoeckert, C. J. and Roos, D. S. (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res., 34, D363-D368.
    • (2006) Nucleic Acids Res. , vol.34 , pp. D363-D368
    • Chen, F.1    Mackey, A.J.2    Stoeckert, C.J.3    Roos, D.S.4
  • 10
    • 84877694192 scopus 로고    scopus 로고
    • Hieranoid: Hierarchical orthology inference
    • Schreiber, F. and Sonnhammer, E. L. L. (2013) Hieranoid: hierarchical orthology inference. J. Mol. Biol., 425, 2072-2081.
    • (2013) J. Mol. Biol. , vol.425 , pp. 2072-2081
    • Schreiber, F.1    Sonnhammer, E.L.L.2
  • 13
    • 84941116885 scopus 로고    scopus 로고
    • InParanoid 8: Orthology analysis between 273 proteomes, mostly eukaryotic
    • Sonnhammer, E. L. L. and Östlund, G. (2015) InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. Nucleic Acids Res., 43, D234-D239.
    • (2015) Nucleic Acids Res. , vol.43 , pp. D234-D239
    • Sonnhammer, E.L.L.1    Östlund, G.2
  • 16
    • 33846067524 scopus 로고    scopus 로고
    • PANTHER version 6: Protein sequence and function evolution data with expanded representation of biological pathways
    • Mi, H., Guo, N., Kejariwal, A. and Thomas, P. D. (2007) PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Res., 35, D247-D252.
    • (2007) Nucleic Acids Res. , vol.35 , pp. D247-D252
    • Mi, H.1    Guo, N.2    Kejariwal, A.3    Thomas, P.D.4
  • 17
    • 78651277241 scopus 로고    scopus 로고
    • MetaPhOrs: Orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score
    • Pryszcz, L. P., Huerta-Cepas, J. and Gabaldón, T. (2011) MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score. Nucleic Acids Res., 39, e32.
    • (2011) Nucleic Acids Res. , vol.39 , pp. e32
    • Pryszcz, L.P.1    Huerta-Cepas, J.2    Gabaldón, T.3
  • 20
    • 33751039720 scopus 로고    scopus 로고
    • Bushes in the tree of life
    • Rokas, A. and Carroll, S. B. (2006) Bushes in the tree of life. PLoS Biol., 4, 1899-1904.
    • (2006) PLoS Biol. , vol.4 , pp. 1899-1904
    • Rokas, A.1    Carroll, S.B.2
  • 22
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Tatusov, R. L., Koonin, E. V. and Lipman, D. J. (1997) A genomic perspective on protein families. Science, 278, 631-637.
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 25
    • 84946069451 scopus 로고    scopus 로고
    • UniProt: A hub for protein information
    • UniProt Consortium. (2015) UniProt: a hub for protein information. Nucleic Acids Res., 43, D204-D212.
    • (2015) Nucleic Acids Res. , vol.43 , pp. D204-D212
    • UniProt Consortium1
  • 26
    • 84891822155 scopus 로고    scopus 로고
    • RefSeq microbial genomes database: New representation and annotation strategy
    • Tatusova, T., Ciufo, S., Fedorov, B., O'Neill, K. and Tolstoy, I. (2014) RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res., 42, D553-D559.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D553-D559
    • Tatusova, T.1    Ciufo, S.2    Fedorov, B.3    O'Neill, K.4    Tolstoy, I.5
  • 29
    • 84891771425 scopus 로고    scopus 로고
    • SIMAP-The database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage
    • Arnold, R., Goldenberg, F., Mewes, H. W. and Rattei, T. (2014) SIMAP-The database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage. Nucleic Acids Res., 42. D279-D284.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D279-D284
    • Arnold, R.1    Goldenberg, F.2    Mewes, H.W.3    Rattei, T.4
  • 30
    • 84941067064 scopus 로고    scopus 로고
    • Expanded microbial genome coverage and improved protein family annotation in the COG database
    • Galperin, M. Y., Makarova, K. S., Wolf, Y. I. and Koonin, E. V. (2015) Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res., 43, D261-D269.
    • (2015) Nucleic Acids Res. , vol.43 , pp. D261-D269
    • Galperin, M.Y.1    Makarova, K.S.2    Wolf, Y.I.3    Koonin, E.V.4
  • 31
    • 84924356749 scopus 로고    scopus 로고
    • Archaeal clusters of Orthologous genes (arCOGs): An update and application for analysis of shared features between thermococcales, methanococcales, and methanobacteriales
    • Makarova, K., Wolf, Y. and Koonin, E. (2015) Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales. Life, 5, 818-840.
    • (2015) Life , vol.5 , pp. 818-840
    • Makarova, K.1    Wolf, Y.2    Koonin, E.3
  • 34
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: A multiple sequence alignment method with reduced time and space complexity
    • Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113.
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 35
    • 33645507429 scopus 로고    scopus 로고
    • M-Coffee: Combining multiple sequence alignment methods with T-Coffee
    • Wallace, I. M., O'Sullivan, O., Higgins, D. G. and Notredame, C. (2006) M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res., 34, 1692-1699.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 1692-1699
    • Wallace, I.M.1    O'Sullivan, O.2    Higgins, D.G.3    Notredame, C.4
  • 36
    • 67650757433 scopus 로고    scopus 로고
    • Trimal: A tool for automated alignment trimming in large-scale phylogenetic analyses
    • Capella-Gutiérrez, S., Silla-Martínez, J. M. and Gabaldón, T. (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25, 1972-1973.
    • (2009) Bioinformatics , vol.25 , pp. 1972-1973
    • Capella-Gutiérrez, S.1    Silla-Martínez, J.M.2    Gabaldón, T.3
  • 38
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
    • Katoh, K. and Standley, D. M. (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
  • 39
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
    • Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W. and Gascuel, O. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol., 59, 307-321.
    • (2010) Syst. Biol. , vol.59 , pp. 307-321
    • Guindon, S.1    Dufayard, J.-F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5    Gascuel, O.6
  • 40
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2-approximately maximum-likelihood trees for large alignments
    • Price, M. N., Dehal, P. S. and Arkin, A. P. (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One, 5, e9490.
    • (2010) PLoS One , vol.5 , pp. e9490
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 41
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated Profile HMM Searches
    • Eddy, S. R. (2011) Accelerated Profile HMM Searches. PLoS Comput. Biol., 7, e1002195.
    • (2011) PLoS Comput. Biol. , vol.7 , pp. e1002195
    • Eddy, S.R.1
  • 42
    • 84946735654 scopus 로고    scopus 로고
    • Gene Ontology Consortium: Going forward
    • Gene Ontology Consortium. (2015) Gene Ontology Consortium: going forward. Nucleic Acids Res., 43, D1049-D1056.
    • (2015) Nucleic Acids Res. , vol.43 , pp. D1049-D1056
    • Gene Ontology Consortium1
  • 45
    • 84946060416 scopus 로고    scopus 로고
    • SMART: Recent updates, new developments and status in 2015
    • Letunic, I., Doerks, T. and Bork, P. (2015) SMART: recent updates, new developments and status in 2015. Nucleic Acids Res., 43, D257-D260.
    • (2015) Nucleic Acids Res. , vol.43 , pp. D257-D260
    • Letunic, I.1    Doerks, T.2    Bork, P.3
  • 52
    • 78650583195 scopus 로고    scopus 로고
    • Assigning duplication events to relative temporal scales in genome-wide studies
    • Huerta-Cepas, J. and Gabaldón, T. (2011) Assigning duplication events to relative temporal scales in genome-wide studies. Bioinformatics, 27, 38-45.
    • (2011) Bioinformatics , vol.27 , pp. 38-45
    • Huerta-Cepas, J.1    Gabaldón, T.2
  • 53
    • 84885647005 scopus 로고    scopus 로고
    • Following gene duplication, paralog interference constrains transcriptional circuit evolution
    • Baker, C. R., Hanson-Smith, V. and Johnson, A. D. (2013) Following gene duplication, paralog interference constrains transcriptional circuit evolution. Science, 342, 104-108.
    • (2013) Science , vol.342 , pp. 104-108
    • Baker, C.R.1    Hanson-Smith, V.2    Johnson, A.D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.