A computational method to search for DNA structural motifs in functional genomic elements.
A computational method to search for DNA structural motifs in functional genomic elements.
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一种在功能基因组元件中搜索 DNA 结构基序的计算方法。
DOI：
10.1007/978-1-61779-173-4_21
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发表时间：
2011
期刊：
影响因子：
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通讯作者：
Tullius,ThomasD
中科院分区：
文献类型：
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作者：
Parker,StephenCJ;Harlap,Aaron;Tullius,ThomasD
从现代高通量实验技术中获得的DNA序列数据的快速增加的可用性已经产生了对计算算法的需求，以帮助在基因组DNA中发现基序。这样的算法通常用于在被认为含有与蛋白质结合的片段的DNA序列集合内找到DNA结合蛋白的靶位点的核苷酸序列的统计表示。这些算法的一个主要假设是蛋白质识别序列中核苷酸的主要顺序。然而，蛋白质也可以识别DNA的三维形状和结构。为了解释这一点，我们开发了一种计算方法来预测任何一组DNA序列的局部结构谱，然后在这些谱中搜索共同的DNA结构基序。在这里，我们描述了这种方法的细节，并使用它来找到一个DNA结构基序在theSaccharomyces gallaeyast基因组，是与结合的转录因子RLM1，蛋白激酶C介导的MAP激酶途径的组成部分。
The rapidly increasing availability of DNA sequence data from modern high-throughput experimental techniques has created the need for computational algorithms to aid in motif discovery in genomic DNA. Such algorithms are typically used to find a statistical representation of the nucleotide sequence of the target site of a DNA-binding protein within a collection of DNA sequences that are thought to contain segments to which the protein is bound. A major assumption of these algorithms is that the protein recognizes the primary order of nucleotides in the sequence. However, proteins can also recognize the three-dimensional shape and structure of DNA. To account for this, we developed a computational method to predict the local structural profiles of any set of DNA sequences and then to search within these profiles for common DNA structural motifs. Here we describe the details of this method and use it to find a DNA structural motif in theSaccharomyces cerevisiaeyeast genome that is associated with binding of the transcription factor RLM1, a component of the protein kinase C-mediated MAP kinase pathway.