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SELEX experiments: new prospects, applications and data analysis in inferring regulatory pathways.

机译：SELEX实验：推断监管途径的新前景，应用和数据分析。

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摘要

Systematic Evolution of Ligands by EXponential enrichment (SELEX) is an experimental procedure that allows extraction, from an initially random pool of oligonucleotides, of the oligomers with a desired binding affinity for a given molecular target. The procedure can be used to infer the strongest binders for a given DNA or RNA binding protein, and the highest affinity binding sequences isolated through SELEX can have numerous research, diagnostic and therapeutic applications. Recently, important new modifications of the SELEX protocol have been proposed. In particular, a modification of the standard SELEX procedure allows generating a dataset from which protein-DNA interaction parameters can be determined with unprecedented accuracy. Another variant of SELEX allows investigating interactions of a protein with nucleic-acid fragments derived from the entire genome of an organism. We review here different SELEX-based methods, with particular emphasis on the experimental design and on the applications aimed at inferring protein-DNA interactions. In addition to the experimental issues, we also review relevant methods of data analysis, as well as theoretical modeling of SELEX.
机译：通过指数富集（SELEX）进行配体的系统进化是一种实验程序，可以从寡核苷酸的初始随机库中提取对指定分子靶具有所需结合亲和力的寡聚物。该程序可用于推断给定DNA或RNA结合蛋白的最强结合物，通过SELEX分离出的最高亲和力结合序列可具有许多研究，诊断和治疗应用。最近，已经提出了对SELEX协议的重要新修改。特别地，对标准SELEX程序的修改允许生成数据集，从中可以以前所未有的精度确定蛋白质-DNA相互作用参数。 SELEX的另一个变体允许研究蛋白质与源自生物体整个基因组的核酸片段的相互作用。我们在这里回顾了不同的基于SELEX的方法，特别着重于实验设计和旨在推断蛋白质与DNA相互作用的应用。除了实验问题之外，我们还回顾了相关的数据分析方法以及SELEX的理论建模。

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