Mariño-Ramírez Leonardo, Tharakaraman Kannan, Spouge John L, Landsman David
Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA.
Methods Mol Biol. 2009;537:263-76. doi: 10.1007/978-1-59745-251-9_13.
Reliable detection of cis-regulatory elements in promoter regions is a difficult and unsolved problem in computational biology. The intricacy of transcriptional regulation in higher eukaryotes, primarily in metazoans, could be a major driving force of organismal complexity. Eukaryotic genome annotations have improved greatly due to large-scale characterization of full-length cDNAs, transcriptional start sites (TSSs), and comparative genomics. Regulatory elements are identified in promoter regions using a variety of enumerative or alignment-based methods. Here we present a survey of recent computational methods for eukaryotic promoter analysis and describe the use of an alignment-based method implemented in the A-GLAM program.
在计算生物学中，可靠地检测启动子区域中的顺式调控元件是一个困难且尚未解决的问题。高等真核生物，主要是后生动物中复杂的转录调控，可能是生物体复杂性的主要驱动力。由于全长cDNA、转录起始位点（TSS）的大规模表征以及比较基因组学，真核生物基因组注释有了很大改进。使用各种枚举或基于比对的方法在启动子区域中识别调控元件。在此，我们概述了近期用于真核生物启动子分析的计算方法，并描述了在A-GLAM程序中实现的基于比对方法的使用。
