ISWAC - PROPOSED SYSTEM FOR THE INTEGRATED ASSEMBLY OF CHROMOSOMES

The generation of a physical map as an integral part of sequence proje ct management is a problem that present computer systems do not addres s. Primarily, the analysis performed is based solely on the informatio n available from a single knowledge level. Management systems that are currently available do not adequately model the multi-layer top down strategy that is most often utilized to manage large scale sequencing projects. Single layered approaches reflect an algorithmic inadequacy since interacting data sets are required to provide a good solution. T he analysis tool that is currently under development termed ISWAC, the Integrated System for Wholistic Assembly of Chromosomes, overcomes th ese limitations by integrating information available from five layers of knowledge. These knowledge layers utilize information from the link age map, physical map, restriction map, clone strategy map and the DNA sequence itself. The approach we are implementing, reviews current pr oject status and continually refines the experimental strategy necessa ry to efficiently complete the sequencing task. To facilitate project completion the system is designed to interactively recommend strategie s based on partial information. The utility of this tool is enhanced b y implementing knowledge representation techniques that allow reasonin g with approximate concepts characteristic of these data-sets. In addi tion, the raw physical data is maintained within an integrated map dat abase to ease data verification. This paper presents the first discuss ion of the design specifications for a computer system to assimilate t he various forms of data that are being generated as part of the human genome project. It was specifically written to stimulate discussion r egarding data standardization, translation, analysis and most importan t, an understandable user-interphase for the molecular biologist. We w ould hope that interested readers would respond by assisting in the de finition of a set of universal data standards anal adopting them in th eir laboratories.