GENEEXPRESS: A COMPUTER SYSTEM FOR DESCRIPTION, ANALYSIS, AND RECOGNITION OF REGULATORY SEQUENCES IN EUKARYOTIC GENOME

Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology, ISMB 1998

Volumn , Issue , 1998, Pages 95-104

  Kolchanov, N A ^a,b   Ponomarenko, M P ^a,b   Kel, A E ^a,b   Kondrakhin, Yu V ^a,b   Frolov, A S ^a,b   Kolpakov, F A ^a,b   Goryachkovsky, T N ^a,b   Kel, O V ^a,b   Ananko, E A ^a,b   Ignatieva, E V ^a,b   Podkolodnaya, O A ^a,b   Babenko, V N ^a,b   Stepanenko, I L ^a,b   Romashchenko, A G ^a,b   Merkulova, T I ^a,b   Vorobiev, D G ^a,b   Laviyushev, S V ^a,b   Ponomarenko, Yu V ^a,b   Kochetov, A V ^a,b   Kolesov, G B ^a,b   Solovyev, V V ^c   Milanesi, L ^d   Podkolodny, N L ^e   Wingender, E ^f   Heinemeyer, T ^f   more..

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b ENERGY SYSTEMS INSTITUTE   (Russian Federation)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^d CNR   (Italy)

^e INSTITUTE OF COMPUTATIONAL MATHEMATICS AND MATHEMATICAL GEOPHYSICS   (Russian Federation)

^f HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

Author keywords

activity; databases; Gene networks; recognition; regulation; site; transcription; translation

Indexed keywords

DATA VISUALIZATION; OBJECT-ORIENTED DATABASES; SIGNAL TRANSDUCTION; TRANSCRIPTION; TRANSLATION (LANGUAGES);

ACTIVITY; EUKARYOTIC GENOME; EUKARYOTICS; GENE NETWORKS; RECOGNITION; REGULATION; REGULATORY SEQUENCES; SITE; TRANSCRIPTION FACTOR BINDING SITES; TRANSLATION;

BINDING SITES;

MESSENGER RNA; TRANSCRIPTION FACTOR;

ARTICLE; ARTIFICIAL INTELLIGENCE; BINDING SITE; COMPUTER PROGRAM; COMPUTER SYSTEM; EUKARYOTIC CELL; FACTUAL DATABASE; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GENOME; METABOLISM; PROTEIN SYNTHESIS; REGULATOR GENE;

ARTIFICIAL INTELLIGENCE; BINDING SITES; COMPUTER SYSTEMS; DATABASES, FACTUAL; EUKARYOTIC CELLS; GENE EXPRESSION REGULATION; GENES, REGULATOR; GENOME; PROTEIN BIOSYNTHESIS; RNA, MESSENGER; SOFTWARE; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 0031609555     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (34)

1. Ananko, E.A., Bazhan, S.I., Belova, O.E., and Kel, A.E. (1997) Mechanisms of transcription of the interferon-induced genes: a description in the IIG-TRRD information system. Mol. Biol (Msk) 31, 701-713.
2. Chen, Q., Hertz, C, and Stormo G. (1995) Matrix search l.o: a computer program that scans D N A sequences for transcriptional elements using a database of weight matrices. C A B I O S 11, 563-566.
3. Etzold, T. and Argos, P. (1993) SRS~an indexing and retrieval tool for flat file data libraries. C A B I O S. 9, 49-57
4. Fickett, J.W. and Hatzigeorgiou, A.G. (1997) Eukaryotic promoter recognition. Genome Res. 7, 861-878.
5. Fishbum, P.C. (1970) Utility Theory for Decision Making, New York: John Wiley & Sons.
6. Isehenko, I.V., Kochetov, A.V., Kel, A.E., Kisselev, L. L., and Kolchanov N.A. (1996) Comparative analysis of the local secondary structure of mRNAs encoded by high- and low-expression eukaryotic genes In: "Proceedings of the German Conference on Bioinformatics (GCB'96). Leipzig Univ.", 124-129.
7. Jonson, J., Norberg, T., Carlsson, L., Gustafsson, C, and Wold, S. (1993) Quantitative sequence-activity models (QSAM) - tools for sequence design. Nucl. Acids Res., 21, 733-739.
8. Kel, A.E. Kondrakhin, Y. V., Kolpakov, Ph.A., Kel, O.V., Romachenko, A.G., Wingender, E., Milanesi, L., and Kolchanov, N.A. (1995) Computer tool F U N S I T E for analysis of eukaryotic regulatory genomic sequences. Proceedings of the third international conference on intelHgent systems for molecular biology. A A A I Press. California. 197- 205.
9. Kel, A.E., Ponomarenko, M.P., Likhachev, E.A., Orlov, Y. L., Isehenko, I.V., Milanesi, L., and Kolchanov, N.A. (1993) SFFEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites. CABIOS. 9, 617-627.
10. Kel, O.V., Romashchenko, A.G., Kel, A.E., Naumochkin, A.N., and Kolchanov, N.A. (1995a) Proceedings of the 28* Annual Hawaii International Conference on System Sciences (HICSSJ. 5. Biotechnology Computing, l E E Computer Society Press: Los Alamos, California. 42 -51
11. Kel, O.V, Romashchenko, A.G., Kel, A.E., Wingender, and E., Kolchanov, N.A., (1995b) A compilation of composite regulatory elements affecting gene transcription in vertebrates. Nucl. Acids Res. 23,4097-4103.
12. K e l ', A. E., Kolchanov, N. A, K e l ', O.V., Romashchenko, A. G., Anan'ko, E. A., Ignati'eva, E. V., Merkulova, T. I., Podkolodnaya, O. A, Stepanenko, I. L., Kochetov, A V, Kolpakov, F. A., Podkolodny, N. L., and Naumochkin A N. (1997) T R R D: database on transcription regulatory regions of eukaryotic genes. Mol. B i o l. (M s k) 3 1, 521-530.
13. Kolchanov, N. A (1997) Regulation of eukaryotic gene transcription: databases and computer analysis. Mol. Biol. (Msk), 31, 481-482.
14. Kolchanov, N.A., Ponomarenko, M.P., Ponomarenko, Yu.V., Podkolodny, N.L., and Frolov, A S. (1998). Functional sites in the prokaryotic and eukaryotic genomes: Computer models and activity predictions. Mol. Biol. (Msk) (in press).
15. Kolpakov, F. A, Ananko, E. A, Kolesov, G.B., and Kolchanov N. A 1998. GeneNet: a database for gene networks and its automated visualization through the Internet. Bioinformatics. (in press.)
16. Kondrakhin, Yu.V., Babenko, V.N., Milanesi, L., Lavryushev, C.V., and Kolchanov, N. A (1998) Recognition groups: a new method for description and prediction and of transcription factor binding sites. CABIOS (in press).
17. Lawrence, C, Altschul, S., Boguski, M., Liu, J., Neuwald, A, and Wootton, J. (1993) Detecting subtle sequence signals: a Gibs sampling strategy for multiple alignment. Science. 262, 208-214.
18. Peter, R.C., Juner, T., and Bucher, P. (1998) The eukaryotic promoter database EPD. Nucl. Acids Res. 26, 353-357.
19. Podkolodnaya, O.A and Stepanenko, I.L. (1997) Mechanisms of transcription regulation of the erythroid-specific genes. Mol. Biol. (Msk), 31, 540-547.
20. Ponomarenko, MP., Kel, A E., Orlov, Y. L., Benjukh, D.N., Isehenko, I.V., Bokhonov, V.B., Likhachev, E. A, and Kolchanov, N. A (1994) Computer Analysis of Genetic Macromolecules: Structure, Function and Evolution (Kolchanov, N. and Lim, H., Eds.) Singapore: World Sci. 35-65
21. Ponomarenko, M.P., Kolchanova, A N., and Kolchanov, N. A (1997b) Generating programs for predicting the activity of functional sites. J. Comput. Biol. 4, 83-90
22. Ponomarenko, M.P., Ponomarenko, Yu.V., Kel', A E., Kolchanov, N.A, Karas, H., Wingender, E., and Sklenar, H. (1997c) Computer analysis of the DNA conformation features of the eukaryotic promoter T A T A box. Mol Biol. (Msk), 31, 733-740.
23. Ponomarenko, M.P., Savinkova, L. K., Ponomarenko, Y u. V, Kel', A E., Titov, I. I., and Kolchanov, N. A (1997a) Modeling TATA-box sequences in eukaryotic genes. Mol. Biol. (Msk), 31, 726-732.
24. Pedersen, A, Baldi, P., Bninak, S., and Chauvin, Y. (1996) Characterization of eukaryotic and prokaryotic promoters using Hiden Markov models. Intel Sys. Mol. B i o l, 4, 182-191.
25. Ptitsyn, A A, Rogozin, I. B., Grigorovich, D. A, Strelets, V. B., Kel', A. E., Milanezi, L., and Kolchanov, N. A (1996) Computer system " A U T O G E N E " for airtomatic analysis of nucleotide sequences. Mol B i o l (Msk), 30, 432-441.
26. Quandt, K., Freeh, K., Karas, H., Wingender, E., and Werner, T. (1995) Matind and Matlnspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucl. Acids. Res. 23, 4878-4884.
27. Salas, F., Haas, J., Brunk, B., Stoeckert Jr, C.J., and Overton, G.C. (1998) EpoDB: a database of genes expressed during vertebrate erythropoiesis. Nucleic Acids Res. 26, 290-292
28. Salamov, AA and Solovyev, V.V. (1997) Recognition of 3'-end cleavage and polyadenylation region of human mRNA precursors. CABIOS 13,23-28.
29. Solovyev, V.V. and Salamov, AA (1997) The Gene-Finder computer tools for analysis of human and model organisms genome sequences. In Proceedings of the Fifth Intemational Conference on Intelligent Systems for Molecular Biology (eds. Rawling C, Clark D., Altman R., Hunter L., Lengauer T., Wodak S.), Halkidiki, Greece, A A A I Press, 294-302
30. Stormo, G.D., Schneider, T.D. and Gold L. (1986) Quantitotive analysis of the relationship between nucleotide sequence and functional activity. Nucl. Acids Res., 14, 6661-6679.
31. Ulyanov, A and Stormo, G. (1995) Multi-alphabet consensus algorithm for identification of low specificity protein-DNA interactions. Nucl. Acids Res. 23, 1434-1440.
32. Waterman, M., Arriata, R., and Galas, D. (1984) Pattern recognition in several sequences. Bull Math Biol, 46, 515-527.
33. Wingender, E., Dietze, P., Karas, H., and Kneuppel, R. (1996) T R A N S F A C: a database on transcription factors and their D N A binding sites. Nucl. Acids Res. 24. P. 238-241.
34. Wingender, E., K e l, A E., K e l, O.V., Karas, H., Heinemeyer, T., Dietze, P., Knüppel, R., Romaschenko, A G., and Kolchanov, N. A (1997) T R A N S F A C, T R R D and C O M P E L: towards a federated database system on transcriptional regulation. Nucleic Acids Res. 25, 265-268