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Volumn 39, Issue 22, 2011, Pages

Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENETICS; BACTERIAL GENOME; BIOINFORMATICS; COMPUTER PROGRAM; ESCHERICHIA COLI; GENE FUSION; GENE MAPPING; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC DATABASE; GLOBAL OPTIMIZATION STRATEGY; HORIZONTAL GENE TRANSFER; INTERNET; ORTHOLOGY; PREDICTION; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

EID: 83755220035     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr766     Document Type: Article
Times cited : (11)

References (22)
  • 1
    • 0014800108 scopus 로고
    • Distinguishing homologous from analogous proteins
    • Fitch,W.M. (1970) Distinguishing homologous from analogous proteins. Syst. Zool., 19, 99-113.
    • (1970) Syst. Zool. , vol.19 , pp. 99-113
    • Fitch, W.M.1
  • 2
    • 37849023306 scopus 로고    scopus 로고
    • Assessing performance of orthology detection strategies applied to eukaryotic genomes
    • Chen,F., Mackey,A.J., Vermunt,J.K. and Roos,D.S. (2007) Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS One, 2, e383.
    • (2007) PLoS One , vol.2
    • Chen, F.1    MacKey, A.J.2    Vermunt, J.K.3    Roos, D.S.4
  • 3
    • 0013017592 scopus 로고    scopus 로고
    • RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
    • Zmasek,C.M. and Eddy,S.R. (2002) RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics, 3, 14.
    • (2002) BMC Bioinformatics , vol.3 , pp. 14
    • Zmasek, C.M.1    Eddy, S.R.2
  • 4
    • 0036173130 scopus 로고    scopus 로고
    • Automated ortholog inference from phylogenetic trees and calculation of orthology reliability
    • Storm,C.E. and Sonnhammer,E.L. (2002) Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics, 18, 92-99. (Pubitemid 34145036)
    • (2002) Bioinformatics , vol.18 , Issue.1 , pp. 92-99
    • Storm, C.E.V.1    Sonnhammer, E.L.L.2
  • 5
    • 36549049268 scopus 로고    scopus 로고
    • Ortholog detection using the reciprocal smallest distance algorithm
    • DOI 10.1385/1-59745-515-6:95, Comparative Genomics
    • Wall,D.P. and Deluca,T. (2007) Ortholog detection using the reciprocal smallest distance algorithm. Methods Mol. Biol., 396, 95-110. (Pubitemid 350190036)
    • (2007) Methods in Molecular Biology , vol.396 , pp. 95-110
    • Wall, D.P.1    DeLuca, T.2
  • 6
    • 55249117540 scopus 로고    scopus 로고
    • An approach of orthology detection from homologous sequences under minimum evolution
    • Kim,K.M., Sung,S., Caetano-Anolles,G., Han,J.Y. and Kim,H. (2008) An approach of orthology detection from homologous sequences under minimum evolution. Nucleic Acids Res., 36, e110.
    • (2008) Nucleic Acids Res. , vol.36
    • Kim, K.M.1    Sung, S.2    Caetano-Anolles, G.3    Han, J.Y.4    Kim, H.5
  • 7
    • 59149102602 scopus 로고    scopus 로고
    • Phylogenetic and functional assessment of orthologs inference projects and methods
    • Altenhoff,A.M. and Dessimoz,C. (2009) Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput. Biol., 5, e1000262.
    • (2009) PLoS Comput. Biol. , vol.5
    • Altenhoff, A.M.1    Dessimoz, C.2
  • 8
    • 80052203057 scopus 로고    scopus 로고
    • QuartetS: A fast and accurate algorithm for large-scale orthology detection
    • Yu,C., Zavaljevski,N., Desai,V. and Reifman,J. (2011) QuartetS: a fast and accurate algorithm for large-scale orthology detection. Nucleic Acids Res., 39, e88.
    • (2011) Nucleic Acids Res. , vol.39
    • Yu, C.1    Zavaljevski, N.2    Desai, V.3    Reifman, J.4
  • 10
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • DOI 10.1126/science.278.5338.631
    • Tatusov,R.L., Koonin,E.V. and Lipman,D.J. (1997) A genomic perspective on protein families. Science, 278, 631-637. (Pubitemid 27464953)
    • (1997) Science , vol.278 , Issue.5338 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 11
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • DOI 10.1006/jmbi.2000.5197
    • Remm,M., Storm,C.E. and Sonnhammer,E.L. (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol., 314, 1041-1052. (Pubitemid 34073068)
    • (2001) Journal of Molecular Biology , vol.314 , Issue.5 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.V.2    Sonnhammer, E.L.L.3
  • 12
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • DOI 10.1101/gr.1224503
    • Li,L., Stoeckert,C.J. Jr and Roos,D.S. (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res., 13, 2178-2189. (Pubitemid 37161775)
    • (2003) Genome Research , vol.13 , Issue.9 , pp. 2178-2189
    • Li, L.1    Stoeckert Jr., C.J.2    Roos, D.S.3
  • 13
    • 38849135019 scopus 로고    scopus 로고
    • Choosing BLAST options for better detection of orthologs as reciprocal best hits
    • DOI 10.1093/bioinformatics/btm585
    • Moreno-Hagelsieb,G. and Latimer,K. (2008) Choosing BLAST options for better detection of orthologs as reciprocal best hits. Bioinformatics, 24, 319-324. (Pubitemid 351189006)
    • (2008) Bioinformatics , vol.24 , Issue.3 , pp. 319-324
    • Moreno-Hagelsieb, G.1    Latimer, K.2
  • 15
    • 33646832750 scopus 로고    scopus 로고
    • Detecting uber-operons in prokaryotic genomes
    • DOI 10.1093/nar/gkl294
    • Che,D., Li,G., Mao,F., Wu,H. and Xu,Y. (2006) Detecting uber-operons in prokaryotic genomes. Nucleic Acids Res., 34, 2418-2427. (Pubitemid 43985679)
    • (2006) Nucleic Acids Research , vol.34 , Issue.8 , pp. 2418-2427
    • Che, D.1    Li, G.2    Mao, F.3    Wu, H.4    Xu, Y.5
  • 16
    • 0033963089 scopus 로고    scopus 로고
    • The ENZYME database in 2000
    • Bairoch,A. (2000) The ENZYME database in 2000. Nucleic Acids Res., 28, 304-305. (Pubitemid 30047788)
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 304-305
    • Bairoch, A.1
  • 18
    • 77955914247 scopus 로고    scopus 로고
    • EGM: Encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes
    • Mahmood,K., Konagurthu,A.S., Song,J., Buckle,A.M., Webb,G.I. and Whisstock,J.C. (2010) EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes. Bioinformatics, 26, 2076-2084.
    • (2010) Bioinformatics , vol.26 , pp. 2076-2084
    • Mahmood, K.1    Konagurthu, A.S.2    Song, J.3    Buckle, A.M.4    Webb, G.I.5    Whisstock, J.C.6
  • 19
    • 33947581390 scopus 로고    scopus 로고
    • The impact of translocations and gene fusions on cancer causation
    • DOI 10.1038/nrc2091, PII NRC2091
    • Mitelman,F., Johansson,B. and Mertens,F. (2007) The impact of translocations and gene fusions on cancer causation. Nat. Rev. Cancer, 7, 233-245. (Pubitemid 46480968)
    • (2007) Nature Reviews Cancer , vol.7 , Issue.4 , pp. 233-245
    • Mitelman, F.1    Johansson, B.2    Mertens, F.3
  • 21
    • 27644472372 scopus 로고    scopus 로고
    • Orthologs, paralogs, and evolutionary genomics
    • DOI 10.1146/annurev.genet.39.073003.114725
    • Koonin,E.V. (2005) Orthologs, paralogs, and evolutionary genomics. Annu. Rev. Genet., 39, 309-338. (Pubitemid 43011118)
    • (2005) Annual Review of Genetics , vol.39 , pp. 309-338
    • Koonin, E.V.1
  • 22
    • 47649104484 scopus 로고    scopus 로고
    • Horizontal gene transfer in eukaryotic evolution
    • Keeling,P.J. and Palmer,J.D. (2008) Horizontal gene transfer in eukaryotic evolution. Nat. Rev. Genet., 9, 605-618.
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 605-618
    • Keeling, P.J.1    Palmer, J.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.