Siddharthan Rahul, van Nimwegen Erik
Institute of Mathematical Sciences, India.
Methods Mol Biol. 2007;395:381-402. doi: 10.1007/978-1-59745-514-5_24.
PhyloGibbs is a program that uses Gibbs sampling to predict putative binding sites for transcription factors in DNA. It has two notable advances over previous algorithms for this task: it handles phylogenetically related sequence systematically, and it evaluates the significance of each predicted site via statistical sampling. In this article, we explain how to use PhyloGibbs effectively. We describe the essential command-line options in detail, and discuss other considerations that arise in practical situations.
PhyloGibbs是一个使用吉布斯采样来预测DNA中转录因子假定结合位点的程序。与之前用于此任务的算法相比，它有两个显著的进步：它系统地处理系统发育相关序列，并且通过统计采样评估每个预测位点的显著性。在本文中，我们解释如何有效地使用PhyloGibbs。我们详细描述了基本的命令行选项，并讨论了实际情况中出现的其他注意事项。
