| Biological organisms can be viewed as a kind of special, information processing systems. In Chapter Two, from this point of view, we give a discussion of the information coding in genomic DNA sequences, which are the biggest information resource in biological cells. Firstly, We focus on the coding methods of protein梒oding regions in genomes. Secondly, after a brief review of the genes expressional regulation at transcription level, we discuss the coding methods of regulatory regions in genomes. Chapter Three presents our theoretical study, by using available open bioinformatics resource on Internet, on a possible coding method of DNA regulatory regions in genomes, which is termed BSP (Base Spatial Pattern) of double梥trand DNA segment. Firstly, We find a 4 and 20 relationship mediated by triple BSP, called 4桞SP?0 relation. We 2 speculate that 4桞SP?0 relation might be a kind of recognition code in some DNA梡rotein interactions. Secondly, The study of experimental data of DNA梡rotein interactions in the gene transcription regulation of eukaryotic cells reveals that the specific recognition of double梙elical nucleic acids by some DNA梑inding proteins might involve BSP. We have found seven sets of experimental data , which were published by other biologists, to support this hypothesis. Finely, We research the formal description of BSP. We find a formal BSP representation that is based on a mathematical model of equivalent classes, and develop a relevant computer梡rocessing algorithm. This representation of BSP is succinct and easily to be processed by computers. More importantly, this representation of BSP provides a method by which BSP or 4桞SP?0 relation can be generalized to single梥trained DNA (ssDNA) and ssDNA梡rotein interactions. Furthermore, BSP or 4桞SP?0 relation can be generalized to RNA (ssDNA) and RNA梡rotein interactions. In Conclusion, we prospect the future of the BSP study.
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