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Core seminar promoter and TF binding site analysis

Intended audience

Users who wish to get an introduction to the central concepts, strategies, and analysis software offered by Genomatix for transcription factor binding site and promoter analysis, and to learn how to apply them most efficiently.

Training concept

Lectures on theoretical background alternate with practical hands-on examples under the guidance of an instructor.


2 days, approx. 6-7 hrs. per day, start on first day: 10:00 am

Number of participants

3 (minimum) up to 6 (maximum)


Intrexon Bioinformatics Germany GmbH, Bayerstr. 85a, 80335 Munich, GERMANY


How do I book?

Contact us at to book a seat or learn more about our seminar schedule.

Please note that there is a 50% discount for academic participants.

Seminar contents

Day 1

  1. Introduction to Genomatix
    • How to get an account
    • Installation / configuration of Genomatix software
    • Genomatix Portal
    • Downloadable help and information
  2. Why genome annotation is important for promoter analysis
    • Overview of ElDorado annotation
    • Genes / loci / transcription units in ElDorado
    • How to get promoter sequences: ElDorado, Gene2Promoter, and Comparative Genomics
    • ElDorado / Gene2Promoter exercises
  3. Transcription factor binding sites (TFBS) basics
    • TFBS structure and function
    • The transcription factor knowledge base: introduction to MatBase
    • Finding physical TF binding sites: MatInspector
    • MatBase / MatInspector exercises
  4. How to define your own TF binding sites de novo
    • MatDefine: generate TFBS definitions from well-known binding sequences
    • CoreSearch: generate TFBS definitions from larger binding regions (e.g. ChIP-on-Chip, ChIP-Seq)
    • MatDefine / CoreSearch exercises

Day 2

  1. Functional promoter analysis
    • Introduction: how functional (not just physical) TF binding sites are defined: regulatory modules
    • FastM: how to create TFBS modules from scratch
    • FrameWorker: automated identification of conserved TFBS frameworks for regulatory module prediction
    • ModelInspector: genome wide search for TFBS frameworks
    • FastM / FrameWorker / ModelInspector exercises
  2. Putting TFBS and their regulatory targets into biological context
    • GeneRanker: biology represented by a set of genes
    • Genomatix Pathway System (GePS): regulatory gene networks
    • GeneRanker / GePS exercises
  3. Analyzing SNP effects on TF binding sites
    • SNPInspector and Large Scale SNP Analysis
    • SNP analysis exercises
  4. Assorted TFBS tools
    • DiAlign / DiAlign TF: local multiple alignment
    • SequenceShaper: promoter design
    • DiAlign / SequenceShaper exercises