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Volumn 33, Issue 3, 2005, Pages 1069-1076

Plant promoter prediction with confidence estimation

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

EID: 14844287054     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki247     Document Type: Article
Times cited : (112)

References (32)
  • 1
    • 0034667792 scopus 로고    scopus 로고
    • Orchestrated response: A symphony of transcription factors for gene control
    • Lemon,B. and Tjian,R. (2000) Orchestrated response: A symphony of transcription factors for gene control. Genes Dev., 14, 2551-2569.
    • (2000) Genes Dev. , vol.14 , pp. 2551-2569
    • Lemon, B.1    Tjian, R.2
  • 2
    • 0033563512 scopus 로고    scopus 로고
    • The biology of eukaryotic promoter prediction - A review
    • Pedersen,A.G., Baldi,P., Chauvin,Y. and Brunak,S. (1999) The biology of eukaryotic promoter prediction - a review. Comput. Chem., 23 191-207.
    • (1999) Comput. Chem. , vol.23 , pp. 191-207
    • Pedersen, A.G.1    Baldi, P.2    Chauvin, Y.3    Brunak, S.4
  • 3
    • 0031579666 scopus 로고    scopus 로고
    • Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes
    • Smale,S.T. (1997) Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes. Biochim. Biophys. Acta, 1351, 73-88.
    • (1997) Biochim. Biophys. Acta , vol.1351 , pp. 73-88
    • Smale, S.T.1
  • 4
    • 0035477896 scopus 로고    scopus 로고
    • Core promoters: Active contributors to combinatorial gene regulation
    • Smale,S.T. (2001) Core promoters: Active contributors to combinatorial gene regulation. Genes Dev., 15, 2503-2508.
    • (2001) Genes Dev. , vol.15 , pp. 2503-2508
    • Smale, S.T.1
  • 5
    • 0032776529 scopus 로고    scopus 로고
    • Models for prediction and recognition of eukaryotic promoters
    • Werner,T. (1999) Models for prediction and recognition of eukaryotic promoters. Mamm. Genome, 10, 168-175.
    • (1999) Mamm. Genome , vol.10 , pp. 168-175
    • Werner, T.1
  • 6
    • 0030669466 scopus 로고    scopus 로고
    • The downstream promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila
    • Burke,T.W. and Kadonaga,J.T. (1997) The downstream promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev., 11, 3020-3031.
    • (1997) Genes Dev. , vol.11 , pp. 3020-3031
    • Burke, T.W.1    Kadonaga, J.T.2
  • 7
    • 0030863002 scopus 로고    scopus 로고
    • Eukaryotic promoter recognition
    • Fickett,J. and Hatzigeorgiou,A. (1997) Eukaryotic promoter recognition. Genome Res., 7, 861-878.
    • (1997) Genome Res. , vol.7 , pp. 861-878
    • Fickett, J.1    Hatzigeorgiou, A.2
  • 8
    • 0033030389 scopus 로고    scopus 로고
    • Interpolated Markov chains for eukaryotic promoter recognition
    • Ohler,U., Harbeck,S., Niemann,H., Noth,E. and Reese,M. (1999) Interpolated Markov chains for eukaryotic promoter recognition. Bioinformatics, 15, 362-369.
    • (1999) Bioinformatics , vol.15 , pp. 362-369
    • Ohler, U.1    Harbeck, S.2    Niemann, H.3    Noth, E.4    Reese, M.5
  • 9
    • 0035252126 scopus 로고    scopus 로고
    • Identification and analysis of eukaryotic promoters: Recent computational approaches
    • Ohler,U. and Niemann,H. (2001) Identification and analysis of eukaryotic promoters: Recent computational approaches. Trends Genet., 17 56-60.
    • (2001) Trends Genet. , vol.17 , pp. 56-60
    • Ohler, U.1    Niemann, H.2
  • 10
    • 0035224747 scopus 로고    scopus 로고
    • Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition
    • Ohler,U., Niemann,H., Lia,G.-C. and Rubin,G.M. (2001) Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics, 17, S199-S206.
    • (2001) Bioinformatics , vol.17
    • Ohler, U.1    Niemann, H.2    Lia, G.-C.3    Rubin, G.M.4
  • 11
    • 0030627562 scopus 로고    scopus 로고
    • The Gene-Finder computer tools for analysis of human and model organisms genome sequences
    • Rawling,C., Clark,D., Altman,R., Hunter,L., Lengauer,T. and Wodak,S. (eds), 21-25 June, Halkidiki, Greece. AAAI Press
    • Solovyev,V.V. and Salamov,A.A. (1997) The Gene-Finder computer tools for analysis of human and model organisms genome sequences. In Rawling,C., Clark,D., Altman,R., Hunter,L., Lengauer,T. and Wodak,S. (eds), Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology, 21-25 June, Halkidiki, Greece. AAAI Press, pp. 294-302.
    • (1997) Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology , pp. 294-302
    • Solovyev, V.V.1    Salamov, A.A.2
  • 12
    • 0033025047 scopus 로고    scopus 로고
    • Promoter 2.0: For the recognition of PolII promoter sequences
    • Knudsen,S. (1999) Promoter 2.0: For the recognition of PolII promoter sequences. Bioinformatics, 15, 356-361.
    • (1999) Bioinformatics , vol.15 , pp. 356-361
    • Knudsen, S.1
  • 14
    • 0036166744 scopus 로고    scopus 로고
    • Dragon promoter finder: Recognition of vertebrate RNA polymerase II promoters
    • Bajic,V.B., Seah,S.H., Chong,A., Zhang,G., Koh,J.L.Y. and Brusic,V. (2002) Dragon promoter finder: Recognition of vertebrate RNA polymerase II promoters. Bioinformatics, 18, 198-199.
    • (2002) Bioinformatics , vol.18 , pp. 198-199
    • Bajic, V.B.1    Seah, S.H.2    Chong, A.3    Zhang, G.4    Koh, J.L.Y.5    Brusic, V.6
  • 15
    • 0002897359 scopus 로고    scopus 로고
    • Large scale sequencing specific neural networks for promoter and splice site recognition
    • Hunter,L. and Klein,T.E. (eds), Biocomputing Proceedings of the 1996 Pacific Symposium, 2-7 January, World Scientific Co., Singapore
    • Reese,M., Harris,N.L. and Eeckman,F.H. (1996) Large scale sequencing specific neural networks for promoter and splice site recognition. In Hunter,L. and Klein,T.E. (eds), Biocomputing Proceedings of the 1996 Pacific Symposium, 2-7 January, World Scientific Co., Singapore.
    • (1996)
    • Reese, M.1    Harris, N.L.2    Eeckman, F.H.3
  • 16
    • 0034737325 scopus 로고    scopus 로고
    • Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: A novel context analysis approach
    • Scherf,M., Klingenhoff,A. and Werner,T. (2000) Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: A novel context analysis approach. J. Mol. Biol. 297, 599-606.
    • (2000) J. Mol. Biol. , vol.297 , pp. 599-606
    • Scherf, M.1    Klingenhoff, A.2    Werner, T.3
  • 17
    • 0036123111 scopus 로고    scopus 로고
    • Computational detection and location of transcription start sites in mammalian genomic DNA
    • Down,T.A. and Hubbard,T.J. (2002) Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res. 12, 458-461.
    • (2002) Genome Res. , vol.12 , pp. 458-461
    • Down, T.A.1    Hubbard, T.J.2
  • 19
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Mouse Genome Sequencing Consortium
    • Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562.
    • (2002) Nature , vol.420 , pp. 520-562
  • 20
    • 18744369030 scopus 로고    scopus 로고
    • The HSA21 Expression Map Initiative A gene expression map of human chromosome 21 orthologues in the mouse
    • The HSA21 Expression Map Initiative (2002) A gene expression map of human chromosome 21 orthologues in the mouse. Nature, 420, 586-590.
    • (2002) Nature , vol.420 , pp. 586-590
  • 21
    • 0042622334 scopus 로고    scopus 로고
    • PromH: Promoters identification using orthologous genomic sequences
    • Solovyev,V. and Shahmuradov,I. (2003) PromH: Promoters identification using orthologous genomic sequences. Nucleic Acids Res., 31, 3540-3545.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3540-3545
    • Solovyev, V.1    Shahmuradov, I.2
  • 24
    • 0037174204 scopus 로고    scopus 로고
    • Prediction algorithms and confidence measures based on algorithmic randomness theory
    • Gammerman,A. and Vovk,V. (2002) Prediction algorithms and confidence measures based on algorithmic randomness theory. Theoret. Comput. Sci., 287, 209-217.
    • (2002) Theoret. Comput. Sci. , vol.287 , pp. 209-217
    • Gammerman, A.1    Vovk, V.2
  • 27
    • 0002656659 scopus 로고    scopus 로고
    • Machine-learning applications of algorithmic randomness
    • Bratko,I. and Dzeroski,S. (eds), 27-30 June, Bled, Slovenia. Morgan Kaufmann, San Francisco, CA
    • Vovk,V., Gammerman,A. and Saunders,C. (1999) Machine-learning applications of algorithmic randomness. In Bratko,I. and Dzeroski,S. (eds), Proceedings of the Sixteenth International Conference on Machine Learning, 27-30 June, Bled, Slovenia. Morgan Kaufmann, San Francisco, CA, pp. 444-453.
    • (1999) Proceedings of the Sixteenth International Conference on Machine Learning , pp. 444-453
    • Vovk, V.1    Gammerman, A.2    Saunders, C.3
  • 29
    • 0034649566 scopus 로고    scopus 로고
    • The Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
    • (2000) Nature , vol.408 , pp. 796-815


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