Using Weeder, Pscan, and PscanChIP for the Discovery of Enriched Transcription Factor Binding Site Motifs in Nucleotide Sequences

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). Curr. Protoc. Bioinform. 47:2.11.1-2.11.31.