Computational identification of transcriptional regulatory elements in DNA sequence.
Computational identification of transcriptional regulatory elements in DNA sequence.
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DOI：
10.1093/nar/gkl372
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发表时间：
2006
影响因子：
14.9
通讯作者：
GuhaThakurta D
中科院分区：
文献类型：
--
作者：
GuhaThakurta D
识别和注释基因组中的所有功能元件，包括基因和调控序列，是基因组学和计算生物学的基本挑战。由于调控元件通常是短的和可变的，它们的识别和发现使用计算算法是困难的。然而，在用于DNA调控元件的建模和检测的计算方法中已经取得了显著的进展。来自多种生物体的完整基因组序列的可用性，以及用于绘制DNA中蛋白质结合位点的mRNA分析和高通量实验方法，有助于开发利用这些辅助数据来告知转录调控元件检测的方法。顺式调控模块和调控序列的高级结构的鉴定也取得了进展，这对于理解后生动物基因组中的转录调控至关重要。本文综述了基因组调控元件建模和识别的计算方法，重点介绍了最近的发展，和当前的挑战。
Identification and annotation of all the functional elements in the genome, including genes and the regulatory sequences, is a fundamental challenge in genomics and computational biology. Since regulatory elements are frequently short and variable, their identification and discovery using computational algorithms is difficult. However, significant advances have been made in the computational methods for modeling and detection of DNA regulatory elements. The availability of complete genome sequence from multiple organisms, as well as mRNA profiling and high-throughput experimental methods for mapping protein-binding sites in DNA, have contributed to the development of methods that utilize these auxiliary data to inform the detection of transcriptional regulatory elements. Progress is also being made in the identification of cis-regulatory modules and higher order structures of the regulatory sequences, which is essential to the understanding of transcription regulation in the metazoan genomes. This article reviews the computational approaches for modeling and identification of genomic regulatory elements, with an emphasis on the recent developments, and current challenges.