Introduction

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).

Publications

  1. MatInspector and beyond: promoter analysis based on transcription factor binding sites.
    Cite this
    Cartharius K, Frech K, Grote K, Klocke B, Haltmeier M, Klingenhoff A, Frisch M, Bayerlein M, Werner T, 2005-07-01 - Bioinformatics (Oxford, England)
  2. MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data.
    Cite this
    Quandt K, Frech K, Karas H, Wingender E, Werner T, 1995-12-01 - Nucleic acids research

Credits

  1. K Cartharius
    Developer

  2. K Frech
    Developer

  3. K Grote
    Developer

  4. B Klocke
    Developer

  5. M Haltmeier
    Developer

  6. A Klingenhoff
    Developer

  7. M Frisch
    Developer

  8. M Bayerlein
    Developer

  9. T Werner
    Investigator

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Summary
AccessionBT006439
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByT Werner