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R. Jothi, S. Cuddapah, A. Barski, et al. Genome-wide identifica-tion of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res., 2008, 36(16): 5221-5231.

被以下文章引用:

• 标题: 高通量测序及读序映射算法的应用High Throughput Sequencing Methods and Applications of Read Mapping Algorithm

  作者: 李慧丽, 何风, 杨航, 郑焱, 吴晓明

  关键字: 蛋白质DNA相互作用, ChIP-Seq, 基因组, 读序映射Protein- DNA Interaction; Chip-Seq; Genome; Sequence Read Mapping

  期刊名称: 《Hans Journal of Biomedicine》, Vol.1 No.1, 2011-05-11

  摘要: 免疫共沉淀-DNA高通量测序二者的结合是研究蛋白质与基因组DNA相互作用及组蛋白修饰的新实验工具，它同时也对短DNA读序在基因组上的映射、映射结果比较提出了新的算法需求。本文介绍新一代测序原理及数据的特点、相关的读序映射算法的基本原理及对应软件，并说明了该方法在组蛋白修饰、转录因子结合位点分析中的应用。Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has become a tool for studying DNA-binding proteins profile and histone modifications. At the same time, it also arouse requirement for ef-fective computational method to map short DNA reads and to compare mapping profiles, which are crucial for uncovering biological mechanisms. In this article, we introduced the principle of new generation se-quencing and corresponding data format, then give an overview of current method of reads mapping and peak identification. Finally, we demonstrated the application of this method in histone modifications analysis and transcription factor binding sites identification.