Molecular Information Theory

信息论是理解定义遗传控制系统的DNA和RNA模式的强大工具。我的理论工作分为几个层次。0级是对蛋白质或其他大分子结合的遗传序列的研究，简要描述如下。这一理论的成功表明，信息论的其他方面也应该适用于分子生物学。1级理论引入了分子机器的更一般的概念，以及机器容量等于香农通道容量的概念。在第二层，热力学第二定律与容量定理相联系。这定义了麦克斯韦恶魔和未来分子计算机的极限。该项目还有三个相互关联的活动：理论、计算机分析和基因工程实验。在0级中，我证明了核酸上的结合位点通常只包含分子在基因组中找到这些位点所需的信息量。这一“工作假说”的明显例外揭示了许多新现象。第一个主要的异常是在噬菌体T7启动子上发现的，它保存的信息量是聚合酶定位它们所需信息量的两倍。最可能的解释是第二种蛋白质与DNA结合。在另一种情况下，我们发现F incD区域有三倍的超额保守性，这意味着有三种蛋白质结合在那里。我们正在对这两种反常现象进行实验研究。已经发明了两种图形方法来显示结合位点的结构。序列标志显示了一组结合位点的平均模式。最近发明的步行器显示了单独的结合位点。同时显示多个步行者已经成为研究遗传结构的强大工具，它无疑将取代共识序列。步行者可以用来区分突变和多态，这有临床应用。请参阅http://www.lecb.ncifcrf.gov/~toms/schneider.html 了解更多信息。

Information theory is a powerful tool for understanding the DNA and RNA patterns that define genetic control systems. My theoretical work is divided into several levels. Level 0 is the study of genetic sequences bound by proteins or other macromolecules, briefly described below. The success of this theory suggested that other aspects of information theory should also apply to molecular biology. Level 1 theory introduces the more general concept of the molecular machine, and the concept of a machine capacity equivalent to Shannon's channel capacity. In Level 2, the Second Law of Thermodynamics is connected to the capacity theorem. This defines the limits of Maxwell's Demon and future molecular computers. The project also has three interrelated activities: theory, computer analysis and genetic engineering experiments. In level 0 I showed that binding sites on nucleic acids usually contain just about the amount of information needed for molecules to find the sites in the genome. Apparent exceptions to this "working hypothesis" have revealed many new phenomena. The first major anomaly was found at bacteriophage T7 promoters, which conserve twice as much information as the polymerase requires to locate them. The most likely explanation is that a second protein binds to the DNA. In another case, we discovered that the F incD region has a three-fold excess conservation, which implies that three proteins bind there. We are investigating both anomalies experimentally. Two graphical methods have been invented to display the structure of binding sites. A sequence logo shows the average patterns in a set of binding sites. The recently invented walker shows individual binding sites. Displaying many walkers simultaneously has become such a powerful tool for investigating genetic structure that it will undoubtedly replace consensus sequences. Walkers can be used to distinguish mutations from polymorphisms, and this has clinical applications. See http://www.lecb.ncifcrf.gov/~toms/schneider.html for further information.