Building integrated systems for data representation and analysis in molecular biology

Biochemical techniques have given to biology experimental tools for sequencing genome fragments. These fragments were of a short length/spl minus/often corresponding to a single gene/spl minus/until the development of extremely fast sequencing methods. Now, large sequencing projects have been started, leading to the availability of huge continuous fragments (300 kBytes for yeast chromosome III). Besides the problem of storing and representing such an amount of data, there is also the fact that the internal organization of these large fragments is often completely unknown. Consecutively, in the near future, the data and knowledge bases dedicated to molecular biology will be most certainly associated with sequence analysis systems in a way to help study the unannotated fragments. We present an example of such association between two biological object-oriented knowledge bases/spl minus/ColiGene (for Escherichia coli) and MultiMap (for mammalian genomes)/spl minus/and two sets of methods that are able to communicate with them: Digit (Dynamics and Interactive Graphical Integrated Tools) and Misa (Modules for Integrated Sequence Analysis). Then we show how it is possible to formalize the methods under an object-oriented knowledge representation model for tasks.<>