ColiGene: object-centered representation for the study of E coli gene expressivity by sequence analysis.

ColiGene is an object-centered knowledge base for the study of gene expressivity in Escherichia coli by DNA sequence analysis. This system was developed with the knowledge base management system SHIRKA. Objects represented in ColiGene are biological structures such as genes or regulatory signals. They are organized in a hierarchical structure of classes, subclasses and instances. Navigation through the knowledge base and the building of queries are made using a graphical interface. The base is coupled with the data base ACNUC which structures a specialized collection of sequences: EcoSeq. Several tools are also associated to ColiGene, either for sequence analysis or for a more general purpose. Some biological results have been obtained using ColiGene which are summarized here.