Sinha Saurabh, Liang Yupu, Siggia Eric
Department of Computer Science, University of Illinois, Urbana-Champaign, NY, USA.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W555-9. doi: 10.1093/nar/gkl224.
Given the DNA-binding specificities (motifs) of one or more transcription factors, an important bioinformatics problem is to discover significant clusters of binding sites for the transcription factors(s). Such clusters often correspond to cis-regulatory modules mediating regulation of an adjacent gene. In earlier work, we developed the Stubb program that uses a probabilistic model and a maximum likelihood approach to efficiently detect cis-regulatory modules over genomic scales. It may optionally exploit a second related genome to improve module prediction accuracy. We describe here the use of a web-based interface for the Stubb program. The interface is equipped with a special post-processing step for in-depth analysis of specific modules, in order to reveal individual binding sites predicted in the module. The web server may be accessed at the URL http://stubb.rockefeller.edu/.
给定一个或多个转录因子的DNA结合特异性（基序），一个重要的生物信息学问题是发现转录因子结合位点的显著聚类。此类聚类通常对应于介导相邻基因调控的顺式调控模块。在早期工作中，我们开发了Stubb程序，该程序使用概率模型和最大似然方法在基因组尺度上高效检测顺式调控模块。它还可以选择利用第二个相关基因组来提高模块预测准确性。我们在此描述Stubb程序基于网络界面的使用。该界面配备了一个特殊的后处理步骤，用于对特定模块进行深入分析，以揭示模块中预测的单个结合位点。可通过URL http://stubb.rockefeller.edu/访问该网络服务器。
