Oligonucleotide frequency matrices addressed to recognizing functional DNA sites

Bioinformatics

Volumn 15, Issue 7-8, 1999, Pages 631-643

  Ponomarenko, Mikhail P ^a   Ponomarenko, Julia V ^a   Frolov, Anatoly S ^a   Podkolodnaya, Olga A ^a   Vorobyev, Denis G ^a   Kolchanov, Nikolay A ^a   Overton, G Christian ^b  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; OLIGONUCLEOTIDE;

ACCURACY; CONFERENCE PAPER; DATA BASE; GENOME; INTERNET; NUCLEIC ACID ANALYSIS; PRIORITY JOURNAL;

EID: 0032822837     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/15.7.631     Document Type: Conference Paper

References (28)

1. Berg, O.G. and von Hippel, P.H. (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol., 193, 723-750.
2. 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.
3. Chen, Q.K., Hertz, G.Z. and Stormo, G.D. (1997) PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices. Comput. Appl. Biosci., 13, 29-35.
4. Etzold, T. and Argos, P (1993) SRS - an indexing and retrieval tool for flat file data libraries. Comput. Appl. Biosci., 9, 49-57.
5. Fickett, J.W. and Hatzigeorgiou, A.G. (1997) Eukaryotic promoter recognition. Genome Res., 7, 861-878.
6. Fishburn, P.C. (1970) Utility Theory for Decision Making. New York, John Wiley & Sons.
7. French, K., Quandt, K. and Werner, T. (1998) Muscle actin genes: a first step towards computational classification of tissue specific promoters. In Silico Biol., 1, 29-38.
8. Gelfand, M. (1995) Prediction of function in DNA sequence analysis. J. Comput. Biol., 2, 87-115.
9. Haussler, D. (1998) Computational genefinding. Trends Guide Bioinf., 1, 12-15.
10. Heinemeyer, T. et al. (1999) Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms. Nucleic Acids Res., 27, 318-322.
11. Karlin, S. and Brendel, V. (1992) Chance and statistical significance in protein and DNA sequence analysis. Science, 257, 39-49.
12. Kel, A.E., Ponomarenko, M.P., Likhachev, E.A., Orlov, Y.L., Ischenko, I.V. Milanesi, L. and Kolchanov, N.A. (1993) SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites. Comput. Appl. Biosci., 9, 617-627.
13. Kolchanov, N.A. et al. (1999) Transcription Regulatory Regions Database (TRRD): its status in 1999. Nucleic Acids Res., 27, 303-306.
14. Kondrakhin, Y.V., Shamin, V.V. and Kolchanov, N.A. (1994) Construction of a generalized consensus matrix for recognition of vertebrate pre-mRNA 3′-terminal processing sites. Comput. Appl. Biosci., 10, 597-603.
15. Kondrakhin, Y.V., Kel, A.E., Kolchanov, N.A., Romashchenko, A.G. and Milanesi, L. (1995) Eukaryotic promoter recognition by binding sites for transcription factors. Comput. Appl. Biosci., 11, 477-488.
16. Lawrence, C. (1994) Toward the unification of sequence and structural data for identification of structural and functional constraints. Comput. Chem., 18, 255-258.
17. Mulligan, M.E., Hawley, D.K., Entriken, R. and McClure, W.R. (1984) Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acids Res., 12, 789-800.
18. Ponomarenko, M.P., Kolchanova, A.N. and Kolchanov, N.A. (1997) Generating programs for predicting the activity of functional sites. J. Comput. Biol., 4, 83-90.
19. Quandt, K., Frech, K., Karas, H., Wingender, E. and Werner, T. (1995) MatInd and MatInspector - New fast and sensitive tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res., 23, 4878-4884.
20. Robison, K., McGuire, A.M. and Church, G.M. (1998) A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Mol. Biol., 284, 241-254.
21. Roulet, E., Fisch, I., Bucher, P. and Mermod, N. (1998) Evaluation of computer tools for prediction of transcription factor binding sites on genomic DNA. In Silico Biol., 1, 21-28.
22. Salgado, H., Santos, A., Garza-Ramos, U., van Helden, J., Diaz, E. and Collado-Vides, J. (1999) RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res., 27, 59-60.
23. Schneider, T.D., Stormo, G.D., Gold, L. and Ehrenfeucht, A. (1986) Information content of binding sites on nucleotide sequences. J. Mol. Biol., 188, 415-431.
24. Stoeckert, C.J., Jr, Salas, F., Brunk, B. and Overton, G.C. (1999) EpoDB: a prototype database for the analysis of genes expressed during vertebrate erythropoiesis. Nucleic Acids Res., 27, 200-203.
25. Wagner, A. (1997) A computational genomics approach to the identification of gene networks. Nucleic Acids Res., 25, 3594-3604.
26. Uberbacher, E.C., Xu, Y. and Mural, R.J. (1996) Discovering and understanding genes in human DNA sequence using GRAIL. Methods Enzymol., 266, 259-281.
27. Zadeh, L.A. (1965) Fuzzi sets. Inf. Control., 8, 338-353.
28. Zhang, M. (1998) A discrimination study of human core-promoters. Pac. Symp. Biocomput., 240-251.