ANALYSIS OF A BACILLUS-SUBTILIS GENOME FRAGMENT USING A COOPERATIVE COMPUTER-SYSTEM PROTOTYPE (REPRINTED FROM GENE-COMBIS, VOL 165, PG GC37-GC51, 1995)

Analysis of the huge volume of data generated by large scale sequencin g projects requires the construction of new, sophisticated computer sy stems. These systems should be able to manage the biological data as w ell as the results of their analysis. They should also help the user t o choose the most appropriate methods, and to string them together in order to solve a global analysis task. In this paper we present the pr ototype of a software system providing an environment for the analysis of large-scale sequence data. As a first step toward this end, this e nvironment has been put to the test within the Bacillus subtilis genom e sequencing project. This system integrates both the descriptive know ledge of the entities involved (genes, regulatory signals and the Like ) and the methodological knowledge comprising an extensible set of ana lytical methods. A knowledge representation based on two existing obje ct-oriented models is used to implement this integrated system. In add ition, the present prototype provides a suitable user interface both f or displaying simultaneously the results generated by several methods and for interacting with the objects. We present in this paper the ana lysis of a B. subtilis genome fragment, present in data libraries but not annotated. Annotation of the genes present in the fragment allowed us to combine the results of several methods used for predicting codi ng sequences, and to characterize it as comprising a cryptic phage, th e skin element. Comparison between the annotation of the skin element and a standard region of the chromosome indicated that local features of the nucleotide sequence could discriminate between phage and non-ph age DNA sequence.