Abstract
Two new databases have been developed to provide the comprehensive research on mechanisms controlling eukaryotic gene expression on the transcription level: TRRD (Transcription Regulatory Region Database) for accumulation of data about structural and functional organisation of gene regulatory regions, and COMPEL - the database on composite regulatory elements that contains contiguous or overlapping binding sites for different transcription factors. Link between TRRD, COMPEL and TRANSFAC through the common table “GENES” has been established. Computer analysis of the transcription regulatory sequences collected in the databases have been carried out by means of SITEVIDEO system. SITEVIDEO offers the following programs: search for significant oligonucleotides in a 15-letter code; dinucleotide weight consensus; analysis of DNA conformation parameters.
This is a preview of subscription content, log in via an institution.
Preview
Unable to display preview. Download preview PDF.
References
Bucher P. The Eukaryotic Promoter Database EPD, EMBL Nucleotide Sequence Data Library, Release 45. (1995) European Bioinformatics Institute, Hinxton Hall, Hinxton, Cambridge CB10 1RQ, United Kingdom.
Gosh D. Status of the transcription factors database (TFD) (1993) Nucl. Acids Res., v.21, pp.3117–3118.
Wingender E., Dietze P., Karas H., and Knüppel R. TRANSFAC: a database on transcription factors and their DNA binding sites (1996). Nucl. Acids Res., 1996, v.24, pp. 238–241.
Kel O.V., Romachenko A.G., Kel A.E., Naumochkin A.N., and Kolchanov N.A. Data representation in the TRRD — a database of transcription regulatory regions of the eukaryotic genomes. (1995) Proceedings of the 28th Annual Hawaii International Conference on System Sciences [HICSS]. Biotechnology Computing, IEE Computer Society Press, Los Alamitos, California, v. 5. pp. 42–51.
Kel O.V., A.G.Romaschenko, A.E.Kel, E.Wingender, N.A.Kolchanov. A compilation of composite regulatory elements affecting gene transcription in vertebrates (1995). Nucl. Acids Res., v.23, pp.4097–4103.
Kel A.E., Kondrakhin Y.V., Kolpakov Ph.A., Kel O.V., Romashenko A.G., Wingender E., Milanesi L., Kolchanov N.A. Computer tool FUNSITE for analysis of eukaryotic regulatory genomic sequences. (1995) Proceedings third International conference on intelligent systems for molecular biology, California, US, pp. 197–205.
Kel A.E., Ponomarenko M.P., Likhachev E., Orlov Yu.L., Ischenko I.V., Milanesi L., Kolchanov N.A. SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites (1993). Comput. Appl. Biosci. v. 9, pp. 617–627.
Karas, H., Knüppel, R., Schulz, W., Sklenar, H. and Wingender, E. Combining structural analysis of DNA with search routines for detection of transcription regulatory elements. (1996) Comput. Appl. Biosci. v. 12, pp. 441–446.
Faisst,S., Meyer, S. Compilation of vertebrate-encoded transcription factors. (1992) Nucl. Acids Res., v. 20, pp. 3–26.
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 1997 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Kel, A.E. et al. (1997). TRRD and COMPEL databases on transcription linked to TRANSFACAS as tools for analysis and recognition of regulatory sequences. In: Hofestädt, R., Lengauer, T., Löffler, M., Schomburg, D. (eds) Bioinformatics. GCB 1996. Lecture Notes in Computer Science, vol 1278. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0033208
Download citation
DOI: https://doi.org/10.1007/BFb0033208
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-63370-9
Online ISBN: 978-3-540-69524-0
eBook Packages: Springer Book Archive