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Volumn 13, Issue 1, 2012, Pages

QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence

Author keywords

Orthologs; Orthology database; Orthology detection

Indexed keywords

ARCHAEAL; COMPARATIVE GENOMICS; COMPLETE GENOMES; CUT-OFF VALUE; DETECTION ACCURACY; EVOLUTIONARY RELATIONSHIPS; GENE DUPLICATIONS; GENE TREE; ORTHOLOGOUS GENES; ORTHOLOGOUS PROTEINS; ORTHOLOGS; ORTHOLOGY; PREDICTION ACCURACY;

EID: 84862578796     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-143     Document Type: Article
Times cited : (11)

References (25)
  • 1
    • 27644472372 scopus 로고    scopus 로고
    • Orthologs, paralogs, and evolutionary genomics
    • 10.1146/annurev.genet.39.073003.114725, 16285863
    • Koonin EV. Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 2005, 39:309-338. 10.1146/annurev.genet.39.073003.114725, 16285863.
    • (2005) Annu Rev Genet , vol.39 , pp. 309-338
    • Koonin, E.V.1
  • 2
    • 33644787447 scopus 로고    scopus 로고
    • OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
    • 1347485, 16381887, Database issue
    • Chen F, Mackey AJ, Stoeckert CJ, Roos DS. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 2006, 34(Database issue):D363-D368. 1347485, 16381887.
    • (2006) Nucleic Acids Res , vol.34
    • Chen, F.1    Mackey, A.J.2    Stoeckert, C.J.3    Roos, D.S.4
  • 3
    • 65449142156 scopus 로고    scopus 로고
    • How confident can we be that orthologs are similar, but paralogs differ?
    • 10.1016/j.tig.2009.03.004, 19368988
    • Studer RA, Robinson-Rechavi M. How confident can we be that orthologs are similar, but paralogs differ?. Trends in genetics: TIG 2009, 25(5):210-216. 10.1016/j.tig.2009.03.004, 19368988.
    • (2009) Trends in genetics: TIG , vol.25 , Issue.5 , pp. 210-216
    • Studer, R.A.1    Robinson-Rechavi, M.2
  • 4
    • 79959828326 scopus 로고    scopus 로고
    • Testing the ortholog conjecture with comparative functional genomic data from mammals
    • 10.1371/journal.pcbi.1002073, 3111532, 21695233
    • Nehrt NL, Clark WT, Radivojac P, Hahn MW. Testing the ortholog conjecture with comparative functional genomic data from mammals. PLoS computational biology 2011, 7(6):e1002073. 10.1371/journal.pcbi.1002073, 3111532, 21695233.
    • (2011) PLoS computational biology , vol.7 , Issue.6
    • Nehrt, N.L.1    Clark, W.T.2    Radivojac, P.3    Hahn, M.W.4
  • 5
    • 0035408587 scopus 로고    scopus 로고
    • Genome annotation: from sequence to biology
    • Stein L. Genome annotation: from sequence to biology. Nat Rev Genet 2001, 2(7):493-503.
    • (2001) Nat Rev Genet , vol.2 , Issue.7 , pp. 493-503
    • Stein, L.1
  • 7
    • 79955765576 scopus 로고    scopus 로고
    • Signalogs: orthology-based identification of novel signaling pathway components in three metazoans
    • 10.1371/journal.pone.0019240, 3086880, 21559328
    • Korcsmaros T, Szalay MS, Rovo P, Palotai R, Fazekas D, Lenti K, Farkas IJ, Csermely P, Vellai T. Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. PLoS One 2011, 6(5):e19240. 10.1371/journal.pone.0019240, 3086880, 21559328.
    • (2011) PLoS One , vol.6 , Issue.5
    • Korcsmaros, T.1    Szalay, M.S.2    Rovo, P.3    Palotai, R.4    Fazekas, D.5    Lenti, K.6    Farkas, I.J.7    Csermely, P.8    Vellai, T.9
  • 8
    • 0036334571 scopus 로고    scopus 로고
    • From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways
    • 10.1128/JB.184.16.4555-4572.2002, 135229, 12142426
    • Gerdes SY, Scholle MD, D'Souza M, Bernal A, Baev MV, Farrell M, Kurnasov OV, Daugherty MD, Mseeh F, Polanuyer BM, et al. From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways. J Bacteriol 2002, 184(16):4555-4572. 10.1128/JB.184.16.4555-4572.2002, 135229, 12142426.
    • (2002) J Bacteriol , vol.184 , Issue.16 , pp. 4555-4572
    • Gerdes, S.Y.1    Scholle, M.D.2    D'Souza, M.3    Bernal, A.4    Baev, M.V.5    Farrell, M.6    Kurnasov, O.V.7    Daugherty, M.D.8    Mseeh, F.9    Polanuyer, B.M.10
  • 9
    • 77957108545 scopus 로고    scopus 로고
    • Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection
    • 10.1186/1471-2105-11-484, 2956735, 20875130
    • Florez AF, Park D, Bhak J, Kim BC, Kuchinsky A, Morris JH, Espinosa J, Muskus C. Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection. BMC Bioinformatics 2010, 11:484. 10.1186/1471-2105-11-484, 2956735, 20875130.
    • (2010) BMC Bioinformatics , vol.11 , pp. 484
    • Florez, A.F.1    Park, D.2    Bhak, J.3    Kim, B.C.4    Kuchinsky, A.5    Morris, J.H.6    Espinosa, J.7    Muskus, C.8
  • 10
    • 0038306149 scopus 로고    scopus 로고
    • Evolution by gene duplication revisited: differentiation of regulatory elements versus proteins
    • Ohta T. Evolution by gene duplication revisited: differentiation of regulatory elements versus proteins. Genetica 2003, 118(2-3):209-216.
    • (2003) Genetica , vol.118 , Issue.2-3 , pp. 209-216
    • Ohta, T.1
  • 11
    • 71749091694 scopus 로고    scopus 로고
    • Evolution by leaps: gene duplication in bacteria
    • 10.1186/1745-6150-4-46, 2787491, 19930658
    • Serres MH, Kerr AR, McCormack TJ, Riley M. Evolution by leaps: gene duplication in bacteria. Biol Direct 2009, 4:46. 10.1186/1745-6150-4-46, 2787491, 19930658.
    • (2009) Biol Direct , vol.4 , pp. 46
    • Serres, M.H.1    Kerr, A.R.2    McCormack, T.J.3    Riley, M.4
  • 12
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • 10.1006/jmbi.2000.5197, 11743721
    • Remm M, Storm CE, Sonnhammer EL. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 2001, 314(5):1041-1052. 10.1006/jmbi.2000.5197, 11743721.
    • (2001) J Mol Biol , vol.314 , Issue.5 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.2    Sonnhammer, E.L.3
  • 13
    • 38549105500 scopus 로고    scopus 로고
    • OrthoDB: the hierarchical catalog of eukaryotic orthologs
    • 2238902, 17947323, Database issue
    • Kriventseva EV, Rahman N, Espinosa O, Zdobnov EM. OrthoDB: the hierarchical catalog of eukaryotic orthologs. Nucleic Acids Res 2008, 36(Database issue):D271-D275. 2238902, 17947323.
    • (2008) Nucleic Acids Res , vol.36
    • Kriventseva, E.V.1    Rahman, N.2    Espinosa, O.3    Zdobnov, E.M.4
  • 14
    • 78651305141 scopus 로고    scopus 로고
    • OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011
    • 3013786, 20972218, Database issue
    • Waterhouse RM, Zdobnov EM, Tegenfeldt F, Li J, Kriventseva EV. OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. Nucleic Acids Res 2011, 39(Database issue):D283-D288. 3013786, 20972218.
    • (2011) Nucleic Acids Res , vol.39
    • Waterhouse, R.M.1    Zdobnov, E.M.2    Tegenfeldt, F.3    Li, J.4    Kriventseva, E.V.5
  • 15
    • 38549137819 scopus 로고    scopus 로고
    • PhylomeDB: a database for genome-wide collections of gene phylogenies
    • 2238872, 17962297, Database issue
    • Huerta-Cepas J, Bueno A, Dopazo J, Gabaldon T. PhylomeDB: a database for genome-wide collections of gene phylogenies. Nucleic Acids Res 2008, 36(Database issue):D491-D496. 2238872, 17962297.
    • (2008) Nucleic Acids Res , vol.36
    • Huerta-Cepas, J.1    Bueno, A.2    Dopazo, J.3    Gabaldon, T.4
  • 16
    • 78651300216 scopus 로고    scopus 로고
    • PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
    • 3013701, 21075798, Database issue
    • Huerta-Cepas J, Capella-Gutierrez S, Pryszcz LP, Denisov I, Kormes D, Marcet-Houben M, Gabaldon T. PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Res 2011, 39(Database issue):D556-D560. 3013701, 21075798.
    • (2011) Nucleic Acids Res , vol.39
    • Huerta-Cepas, J.1    Capella-Gutierrez, S.2    Pryszcz, L.P.3    Denisov, I.4    Kormes, D.5    Marcet-Houben, M.6    Gabaldon, T.7
  • 17
    • 38549177928 scopus 로고    scopus 로고
    • EggNOG: automated construction and annotation of orthologous groups of genes
    • 2238944, 17942413, Database issue
    • Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res 2008, 36(Database issue):D250-D254. 2238944, 17942413.
    • (2008) Nucleic Acids Res , vol.36
    • Jensen, L.J.1    Julien, P.2    Kuhn, M.3    von Mering, C.4    Muller, J.5    Doerks, T.6    Bork, P.7
  • 18
    • 75549085495 scopus 로고    scopus 로고
    • EggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
    • 2808932, 19900971, Database issue
    • Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, et al. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res 2010, 38(Database issue):D190-D195. 2808932, 19900971.
    • (2010) Nucleic Acids Res , vol.38
    • Muller, J.1    Szklarczyk, D.2    Julien, P.3    Letunic, I.4    Roth, A.5    Kuhn, M.6    Powell, S.7    von Mering, C.8    Doerks, T.9    Jensen, L.J.10
  • 19
    • 78651316211 scopus 로고    scopus 로고
    • OMA 2011: orthology inference among 1000 complete genomes
    • 3013747, 21113020, Database issue
    • Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C. OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res 2011, 39(Database issue):D289-D294. 3013747, 21113020.
    • (2011) Nucleic Acids Res , vol.39
    • Altenhoff, A.M.1    Schneider, A.2    Gonnet, G.H.3    Dessimoz, C.4
  • 20
    • 80052203057 scopus 로고    scopus 로고
    • QuartetS: a fast and accurate algorithm for large-scale orthology detection
    • 10.1093/nar/gkr308, 3141274, 21572104
    • Yu C, Zavaljevski N, Desai V, Reifman J. QuartetS: a fast and accurate algorithm for large-scale orthology detection. Nucleic Acids Res 2011, 39(13):e88. 10.1093/nar/gkr308, 3141274, 21572104.
    • (2011) Nucleic Acids Res , vol.39 , Issue.13
    • Yu, C.1    Zavaljevski, N.2    Desai, V.3    Reifman, J.4
  • 21
    • 59149102602 scopus 로고    scopus 로고
    • Phylogenetic and functional assessment of orthologs inference projects and methods
    • 10.1371/journal.pcbi.1000262, 2612752, 19148271
    • Altenhoff AM, Dessimoz C. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS computational biology 2009, 5(1):e1000262. 10.1371/journal.pcbi.1000262, 2612752, 19148271.
    • (2009) PLoS computational biology , vol.5 , Issue.1
    • Altenhoff, A.M.1    Dessimoz, C.2
  • 22
    • 58149178579 scopus 로고    scopus 로고
    • NCBI Reference Sequences: current status, policy and new initiatives
    • 2686572, 18927115, Database issue
    • Pruitt KD, Tatusova T, Klimke W, Maglott DR. NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res 2009, 37(Database issue):D32-D36. 2686572, 18927115.
    • (2009) Nucleic Acids Res , vol.37
    • Pruitt, K.D.1    Tatusova, T.2    Klimke, W.3    Maglott, D.R.4
  • 23
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • 10.1093/nar/30.7.1575, 101833, 11917018
    • Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002, 30(7):1575-1584. 10.1093/nar/30.7.1575, 101833, 11917018.
    • (2002) Nucleic Acids Res , vol.30 , Issue.7 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 24
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: identification of ortholog groups for eukaryotic genomes
    • 10.1101/gr.1224503, 403725, 12952885
    • Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003, 13(9):2178-2189. 10.1101/gr.1224503, 403725, 12952885.
    • (2003) Genome Res , vol.13 , Issue.9 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 25
    • 47049086792 scopus 로고    scopus 로고
    • PhyloWidget: web-based visualizations for the tree of life
    • 10.1093/bioinformatics/btn235, 18487241
    • Jordan GE, Piel WH. PhyloWidget: web-based visualizations for the tree of life. Bioinformatics 2008, 24(14):1641-1642. 10.1093/bioinformatics/btn235, 18487241.
    • (2008) Bioinformatics , vol.24 , Issue.14 , pp. 1641-1642
    • Jordan, G.E.1    Piel, W.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.