Recognition of eukaryotic promoters using a genetic algorithm based on iterative discriminant analysis

In Silico Biology

Volumn 3, Issue 1-2, 2003, Pages 81-87

  Levitsky, Victor G ^a   Katokhin, Alexey V ^a  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

Author keywords

Dinucleotide frequencies; Discriminant analysis; DPE containing promoters; Eurkaryotic promoter recognition; Genetic algorithm; Nucleosome formation potential; Promoter region partition; TATA containing promoters

Indexed keywords

DINUCLEOTIDE; TATA BINDING PROTEIN;

BACTERIAL GENE; COMPUTER PROGRAM; CONFERENCE PAPER; DISCRIMINANT ANALYSIS; DROSOPHILA MELANOGASTER; EUKARYOTE; GENE EXPRESSION SYSTEM; GENE FREQUENCY; GENE MUTATION; GENETIC ALGORITHM; GENETIC ANALYSIS; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOSOME; PROMOTER REGION;

ALGORITHMS; ANIMALS; BINDING SITES; DISCRIMINANT ANALYSIS; DROSOPHILA MELANOGASTER; MODELS, GENETIC; PROMOTER REGIONS (GENETICS); RECOMBINATION, GENETIC; TATA BOX;

EID: 0042889134     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (17)

1. Bucher, P. (1990). Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol. 212, 563-578.
2. Davuluri, R. V., Grosse, I. and Zhang, M. Q. (2001). Computational identification of promoters and first exons in the human genome. Nat. Genet. 29, 412-417.
3. Goodrich, J. A., Cutler, G. and Tjian, R. (1996). Contacts in context: Promoter specificity and macromolecular interactions in transcription. Cell 84, 825-830.
4. Hannenhalli, S. and Levy, S. (2001). Promoter prediction in the human genome. Bioinformatics 17 Suppl. 1, S90-S96.
5. Katokhin, A. V. and Levitsky, V. G. (2000). Drosophila Promoter Database EnDPD: Project and the first steps of its realization. In: Proc. 2nd Int. Conf. on Bioinformatics of Genome Regulation and Structure BGRS'2002, Kolchanov, N. A. et al. (eds.), Novosibirks, III, pp. 105-108.
6. Knudsen, S. (1999). Promoter2.0: For the recognition of PolII promoter sequences. Bioinformatics 15, 356-361.
7. Kolchanov, N. A., Ignatieva, E. V., Ananko, E. A., Podkolodnaya, O. A., Stepanenko, I. L., Merkulova, T. I., Pozdnyakov, M. A., Podkolodny, N. L., Naumochkin, A. N. and Romashchenko, A. G. (2002). Transcription Regulatory Regions Database (TRRD): Its status in 2002. Nucleic Acids Res. 30, 312-317.
8. Kutach, A. K. and Kadonaga, J. T. (2000). The downstream promoter element DPE appears to be as widely used as the TATA box in Drosphila core promoters. Mol. Cell. Biol. 20, 4754-4764.
9. Levitskii, V. G. and Katokhin, A. V. (2001). Computer analysis and recognition of Drosophila melanogaster gene promoters. Mol. Biol. (Mosk.) 35, 970-978.
10. Levisky, V. G., Podkolodnaya, O. A., Kolchanov, N. A. and Podkolodny, N. L. (2001a). Nucleosome formation potential of eukaryotic DNA: Tools for calculation and promoters analysis. Bioinformatics 17, 998-1010.
11. Levitsky, V. G., Podkolodnaya, O.A., Kolochanov, N. A. and Podkolodny, N. L. (2001b). Nucleosome formation potential of exons, introns, and Alu repeats. Bioinformatics 17, 1062-1067
12. Mahalanobis, P. C. (1936). On the generalised distance in statistics. Proc. Natl. Inst. Sci. India 12, 49-55.
13. Ohler, U., Harbeck, S., Niemann, H., Noth, E. and Reese, M. G. (1999). Interpolated Markov chains for eukaryotic promoter recognition. Bioinformatics 15, 362-369.
14. Ohler, U., Niemann, H., Liao, G. and Rubin, G. M. (2001). Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics 17 Suppl. 1, S199-S206.
15. Ohler, U., Liao, G. C., Niemann, H. and Rubin, G. M. (2002). Computational analysis of core promoters in the Drosophila genome. Genome Biol. 3, research0087.1-0087.12.
16. Reese, M. G. (2001). Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput. Chem. 26, 51-56.
17. Willett, P. (1995). Genetic algorithms in molecular recognition and design. Trends Biotechnol. 13, 516-521.