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A Factor-Space Approach to Genome Analysis

With the staggering amount of gene and protein sequence information that is now available it is evident that the dynamics of biological regulatory mechanisms cannot be understood by merely identifying components, cataloguing products and ensembles. The aim of this paper is to outline a formal mathematical framework which maps sample sequence and derived secondary data onto existing model genomes, metabolic, regulatory and developmental pathways in genome analysis. Apart from a conceptual framework (which we refer to as fuzzy relational biology), the objective is to develop a working methodology for the analysis of genomes in terms of gene expression. The representation of biological knowledge (concepts, facts, and rules) is based on results in the mathematics of fuzzy mappings. Keywords—Genome Analysis, Factor-Space Models, Fuzzy Mathematics, System Theory.