No systematic method exists to derive inter-nucleosomal potentials between nucleosomes along a chromosome consistently across a given genome. Such potentials can yield information on nucleosomal ordering, thermal as well as mechanical properties of chromosomes. Thus, indirectly, they shed light on a possible mechanical genomic code along a chromosome. To develop a method yielding effective inter-nucleosomal potentials between nucleosomes, a generalized Lennard-Jones potential for the parameterization is developed based on nucleosomal positioning data. This approach eliminates some of the problems that the underlying nucleosomal positioning data have, rendering the extraction difficult on the individual nucleosomal level. Furthermore, patterns on which to base a classification along a chromosome appear on larger domains, such as hetero- and euchromatin. An intuitive selection strategy for the noisy optimization problem is employed to derive effective exponents for the generalized potential. The method is tested on the Candida albicans genome. Applying k-means clustering based on potential parameters and thermodynamic compressibilities, a genome-wide clustering of nucleosome sequences is obtained for C. albicans. This clustering shows that a chromosome beyond the classical dichotomic categories of hetero- and euchromatin is more feature-rich.

中文翻译：

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来自核小体定位数据的核小体间电位。

没有系统的方法可以在给定的基因组中始终如一地推导沿染色体的核小体之间的核小体间电位。这种电位可以产生关于染色体的核小体排序、热以及机械特性的信息。因此，间接地，他们揭示了染色体上可能的机械基因组密码。为了开发一种在核小体之间产生有效的核小体间电位的方法，基于核小体定位数据开发了用于参数化的广义 Lennard-Jones 电位。这种方法消除了潜在的核小体定位数据所具有的一些问题，使得在单个核小体水平上的提取变得困难。此外，沿着染色体进行分类的模式出现在更大的域上，例如异染色质和常染色质。噪声优化问题的直观选择策略用于推导广义势的有效指数。该方法在白色念珠菌基因组上进行了测试。应用基于潜在参数和热力学可压缩性的 k-means 聚类，获得白色念珠菌的全基因组核小体序列聚类。这种聚类表明，超出经典的异染色质和常染色质二分法类别的染色体具有更丰富的特征。获得了白色念珠菌的全基因组核小体序列聚类。这种聚类表明，超出经典的异染色质和常染色质二分法类别的染色体具有更丰富的特征。获得了白色念珠菌的全基因组核小体序列聚类。这种聚类表明，超出经典的异染色质和常染色质二分法类别的染色体具有更丰富的特征。