Faster results, better answers, more biology.

Genomatix Software Suite

A well-established software bundle, the Genomatix Software Suite performs a number of tasks:

  • conducts a scientific analysis of genomic data, gene regulation and expression
  • generates and evaluates networks and pathways
  • performs extended literature searches and sequence analyses and extraction
  • visualizes our comprehensive genome annotation.
Thanks to the suite's modular design, programs can be licensed selectively. This means individual

solutions come tailored to your requirements. Whatever you need – a single account or company-wide access – the suite offers as much flexibility and choice as you want.

But what makes the Genomatix Suite such a convenient and efficient tool for every researcher? No matter where you sit, the suite's integrated, online user interface puts universal data access at your fingertips. And you can seamlessly transfer your results from one module to another.


Modules of the Genomatix Software Suite

NGS Mapping
(available on GGA only)
  • Extremely fast and flexible mapping algorithm, allowing for multiple insertions or deletions.
  • Mapping to genomes and transcriptomes of 33 organisms.
  • Detection of known and de-novo splicing events.
  • Support for bisulfite sequencing reads.
  • For genome mappings, Bowtie2 is supported in addition to the Genomatix Mapper.
  • Statistics and classification of reads based on our excellent proprietary genome annotation.

Gene Regulation
  • Detection of transcription factor binding site motifs using our renowned MatInspector software
  • MatBase, our transcription factor knowledge base, containing thousands of transcription factors, weight matrix descriptions, gene-gene interactions, literature citations and more
  • Identification of common transcription factor binding sites in sets of multiple sequences
  • Gene regulation analyses, alignments, definition and search of complex regulatory patterns can easily and extensively performed using the various tasks within GEMS Launcher
  • Search for overrepresented transcription factor binding sites in sets of multiple sequences

Literature & Pathways
  • Generation and Visualization of pathways, networks and processes
  • Association of user data with verified regulatory, pathway and literature data for genes, proteins and interactions, diseases, small molecules
  • Overlay gene expression data from separate timepoints or conditions on networks or pathways and visualize associated metadata like methylation or histone modifications
  • Pathways can be extended individually and exported for publications (print or web) or subsequent analyses (XML based)
  • Use LitInspector to quickly obtain information on genes, gene correlations, pathways, diseases, tissues and small molecules from published literature
  • Characterize gene sets based on annotation and literature (pathways, GO & MeSH terms, small molecules, and more)

NGS Analysis
(available on GGA only)
  • Complete ChIP-Seq workflow that runs peak-calling (including differential analysis on multiple files), motif-generation, comparison to existing binding patterns and identification of overrepresented transcription factor binding sites in called regions in a single run.
  • Stand-alone peak calling using various established algorithms.
  • Expression analysis of RNA-Seq data using various established algorithms.
  • microRNA analysis.
  • Small variant detection (based on samtools).
  • Prediction of structural variants.

Results from the NGS Analysis tasks can immediately be used within the other modules: e.g. differentially expressed genes to run an analysis in the Genomatix Pathway System.

Genes & Genomes
  • Retrieval and Visualization of our first class genome annotation for 33 different organisms
  • Upload and visualization of user data within the ElDorado Annotation in our feature-rich GenomeBrowser
  • Extraction of single or up to thousands of promoter sequences in combination with transcription factor analysis
  • Visualization of alternative transcripts, splice-sites, novel transcripts and gene fusions in TranscriptomeViewer
  • Variant analysis (including detection of amino acid changes and changes in transcription factor binding sites)
  • Identification of orthologous regions within the available organisms
  • Association of genomic features / positions to detect distance based correlations using GenomeInspector