MatInspector and beyond: promoter analysis based on transcription factor binding sites

TLDR

Promoter analysis, essential for mapping regulatory networks, depends on accurate transcription factor binding site predictions, which enable subsequent steps such as detecting phylogenetically conserved patterns or higher‑order site combinations in co‑regulated genes. The authors present an updated MatInspector program that identifies transcription factor binding sites using a large weight‑matrix library, and describe additional tools (DiAlignTF, FrameWorker, SequenceShaper) for in‑depth promoter analysis and regulatory sequence design. The enhanced MatInspector introduces a matrix‑family concept, optimized thresholds, and comparative analysis to produce concise, non‑redundant TFBS predictions, and the authors also provide related tools (DiAlignTF, FrameWorker,.

Abstract

Promoter analysis is an essential step on the way to identify regulatory networks. A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites (TFBS) with reasonable accuracy. The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes.We present a new version of the program MatInspector that identifies TFBS in nucleotide sequences using a large library of weight matrices. By introducing a matrix family concept, optimized thresholds, and comparative analysis, the enhanced program produces concise results avoiding redundant and false-positive matches. We describe a number of programs based on MatInspector allowing in-depth promoter analysis (DiAlignTF, FrameWorker) and targeted design of regulatory sequences (SequenceShaper).