Three models of gene regulation in E. coli
We have initiated the construction of a database on the regulation of transcription initiation in E. coli. In this chapter we discuss three alternative designs of this database. The first model is based on considering promoters, and binding sites for regulators, as objects, and the regulatory interaction as a function linking essentially three objects: the regulatory protein, the site, and the regulated promoter. The second model is based on considering the notions of promoters, sites and genes, as functional properties mapped on specific sequences. Their associated physical sequences are no more considered DNA sequences with inherent properties. Finally, the third model emphasizes the different levels of representation that can be used to describe gene regulation. The selection of a representation among several alternatives is found when designing a database as well as when building grammatical models. Taking this notational problem seriously may help to a better biological insight of the process being modelled.
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