Imagene: an integrated computer environment for sequence annotation and analysis

Motivation: To be fully and efficiently exploited, data coming from sequenc ing projects together with specific sequence analysis tools need to be inte grated within reliable data management systems. Systems designed to manage genome data and analysis tend to give a greater importance either to the da ta storage or to the methodological aspect, but lack a complete integration of both components. Results: This paper presents a co-operative computer environment (called Im agine(TM)) dedicated to genomic sequence analysis an object-based model. Th anks to this representation, the user can directly manipulate familiar data objects through icons or lists. Imagine also incorporates a solving engine in order to manage analysis tasks. A global task is solved by successive d ivisions into smaller sub-tasks. During program execution, these sub-tasks are graphically displayed to the user and may be further re-started at any point after task completion. In this sense, Imagine is more transparent to the user than a traditional menu-driven package. Imagine also provides a us er interface to display, on the same screen, the results produced by severa l tasks, together with the capability to annotate these results easily. In its current form, Imagine has been designed particularly for use in microbi al sequencing projects. Availability: Imagine best runs on SGI (Irix 6.3 or higher) workstations. I t is distributed free of charge on a CD-ROM, but requires some Ilog license d software to run. Some modules also require separate license agreements. P lease contact the authors for specific academic conditions and other Unix p latforms. Contact: imagine@abi.snv.jussieu.fr;imagine home page: http://wwwabi.snv.ju ssieu.fr/imagine.