Zambelli Federico, Pesole Graziano, Pavesi Giulio
Dipartimento di Bioscienze, Università di Milano, Italy; Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Italy.
Curr Protoc Bioinformatics. 2014 Sep 8;47:2.11.1-31. doi: 10.1002/0471250953.bi0211s47.
One of the greatest challenges facing modern molecular biology is understanding the complex mechanisms regulating gene expression. A fundamental step in this process requires the characterization of sequence motifs involved in the regulation of gene expression at transcriptional and post-transcriptional levels. In particular, transcription is modulated by the interaction of transcription factors (TFs) with their corresponding binding sites. Weeder, Pscan, and PscanChIP are software tools freely available for noncommercial users as a stand-alone or Web-based applications for the automatic discovery of conserved motifs in a set of DNA sequences likely to be bound by the same TFs. Input for the tools can be promoter sequences from co-expressed or co-regulated genes (for which Weeder and Pscan are suitable), or regions identified through genome wide ChIP-seq or similar experiments (Weeder and PscanChIP). The motifs are either found by a de novo approach (Weeder) or by using descriptors of the binding specificity of TFs (Pscan and PscanChIP).
现代分子生物学面临的最大挑战之一是理解调控基因表达的复杂机制。这一过程的一个基本步骤需要对参与转录和转录后水平基因表达调控的序列基序进行表征。特别是，转录是由转录因子（TFs）与其相应结合位点的相互作用调节的。Weeder、Pscan和PscanChIP是免费提供给非商业用户的软件工具，可作为独立应用程序或基于网络的应用程序，用于自动发现一组可能被相同TFs结合的DNA序列中的保守基序。这些工具的输入可以是来自共表达或共调控基因的启动子序列（Weeder和Pscan适用），或者是通过全基因组ChIP-seq或类似实验鉴定的区域（Weeder和PscanChIP）。这些基序要么通过从头开始的方法（Weeder）找到，要么通过使用TFs结合特异性的描述符（Pscan和PscanChIP）找到。
