Interpolated Markov chains for eukaryotic promoter recognition

Bioinformatics

Volumn 15, Issue 5, 1999, Pages 362-369

  Ohler, Uwe ^a,b   Harbeck, Stefan ^a   Niemann, Heinrich ^a   Nöth, Elmar ^a   Reese, Martin G ^b  

^a UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG;

ARTICLE; CODON; DNA SEQUENCE; EUKARYOTE; HUMAN; PRIORITY JOURNAL; PROBABILITY; PROMOTER REGION;

EID: 0033030389     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/15.5.362     Document Type: Article

References (20)

1. Audic, S. and Claverie, J.-M. (1997) Detection of eukaryotic promoters using Markov transition matrices. Comput. Chem., 21, 223-227.
2. Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
3. Burge, C. and Karlin, S. (1998) Finding the genes in genomic DNA. Curr. Opin. Struct. Biol., 8, 346-354.
4. Dempster, A.P., Laird, N.M. and Rubin, D.B. (1977) Maximum Likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc., 39, 1-38.
5. Fickett, J.W. and Hatzigeorgiou, A.G. (1997) Eukaryotic promoter recognition. Genome Res., 7, 861-878.
6. Fickett, J.W. and Tung, C.-S. (1992) Assessment of protein coding measures. Nucleic Acids Res., 20, 6441-6450.
7. Frech, K., Quandt, K. and Werner, T. (1998) Muscle actin genes: a first step towards computational classification of tissue specific promoters. In Silico Biol., 1. http://www.bioinfo.de/isb/1998/01/0005/.
8. Hutchinson, G.B. (1996) The prediction of vertebrate promoter regions using differential hexamer frequency analysis. Comput. Applic. Biosci., 12, 391-398.
9. Kornberg, R.D. (1996) RNA polymerase II transcription control. Trends Biochem. Sci., 21, 325-326.
10. Krogh, A. (1997) Two methods for improving performance of an HMM and their application for gene finding. In Proceedings of the Fifth International Conference on Intelligent Systems in Molecular Biology. AAAI Press, Menlo Park, pp. 179-186.
11. Kulp, D., Haussler, D., Reese, M.G. and Eeckman, F.H. (1996) A generalized hidden Markov model for the recognition of human genes in DNA. In Proceedings of the Fourth International Conference on Intelligent Systems in Molecular Biology, St Louis. Menlo Park, pp. 134-142.
12. Lukashin, A.V. and Borodovsky, M. (1998) GeneMark. hmm: new solutions for gene finding. Nucleic Acids Res., 26, 1107-1115.
13. Nikolov, D.B. and Burley, S.K. (1997) RNA polymerase II transcription initiation: A structural view. Proc. Natl Acad. Sci. USA, 94, 15-22.
14. Ohler, U. and Reese, M.G. (1998) Detection of eukaryotic promoter regions using stochastic language models. In Hofestädt, R. (ed.), Molekulare Bioinformatik. Shaker, Aachen, pp. 89-100.
15. Perier, R.C., Junier, T. and Bucher, P. (1998) The Eukaryotic Promoter Database EPD. Nucleic Acids Res., 26, 353-357.
16. Reese, M.G. and Eeckman, F.H. (1998) Time-delay neural networks for eukaryotic promoter prediction. Submitted. See http://www-hgc.lbl.gov/projects/promoter.html
17. Reese, M.G., Eeckman, F.H., Kulp, D. and Haussler, D. (1997) Improved splice site detection in GENIE. J. Comput. Biol., 4, 311-323.
18. Salzberg, S.L., Delcher, A.L., Kasif, S. and White, O. (1998) Microbial gene identification using interpolated Markov models. Nucleic Acids Res., 26, 544-548.
19. Schukat-Talamazzini, E.G., Gallwitz, F., Harbeck, S. and Warnke, V. (1997) Rational interpolation of Maximum Likelihood predictors in stochastic language modeling. In Proceedings of a European Conference on Speech Communication and Technology. Rhodes, Greece, pp. 2731-2734.
20. Solovyev, V. and Salamov, A. (1997) The Gene-Finder computer tools for analysis of human and model organisms genome sequences. In Proceedings of the Fifth International Conference on Intelligent Systems in Molecular Biology. AAAI Press, Menlo Park, pp. 294-302.