Collado-Vides J
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.
Comput Appl Biosci. 1991 Jul;7(3):321-6. doi: 10.1093/bioinformatics/7.3.321.
No one questions the important practical contributions of computer sciences to molecular biology. It may well be that one day theoretical contributions also will become useful. One example of this type of interdisciplinary research is the attempt to construct a grammatical theory of the regulation of gene expression. In this paper, I demonstrate that context-free grammars are inadequate for the description of regulatory properties coded in the DNA. This result is supported by data available in the literature that show changes in the specificity of the recognition between regulatory proteins and their DNA targets. This result is an important limitation for the use of statistical approaches such as information theory as a source of inspiration for a theory of gene regulation. Additionally, such a demonstration gives formal justification to the search for more elaborate grammatical models in the study of gene regulation. Some basic proposals for such grammatical approach have been presented previously.
没有人质疑计算机科学对分子生物学做出的重要实际贡献。很有可能有一天理论贡献也会变得有用。这种跨学科研究的一个例子是尝试构建一种基因表达调控的语法理论。在本文中，我证明上下文无关语法不足以描述DNA中编码的调控特性。文献中可用的数据支持了这一结果，这些数据显示了调控蛋白与其DNA靶点之间识别特异性的变化。这一结果对于使用诸如信息论等统计方法作为基因调控理论的灵感来源是一个重要限制。此外，这样的证明为在基因调控研究中寻找更精细的语法模型提供了形式上的依据。此前已经提出了一些关于这种语法方法的基本建议。
