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

Bioinformatics. 2005 Jul 1;21(13):2933-42. doi: 10.1093/bioinformatics/bti473. Epub 2005 Apr 28.


Motivation: 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.

Results: 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).

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Base Sequence
  • Binding Sites
  • Conserved Sequence
  • Molecular Sequence Data
  • Promoter Regions, Genetic / genetics*
  • Protein Binding
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods*
  • Sequence Homology, Nucleic Acid
  • Software
  • Transcription Factors / genetics*
  • Transcription, Genetic / genetics*


  • Transcription Factors