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Genomatix Genome Analyzer (GGA)

The Genomatix Genome Analyzer (GGA) is our integrated solution for comprehensive visualization and interpretation of Next Generation Sequencing (NGS) data from ChIP, RNA, DNA, methylation or small RNA sequencing. Each analyzer is brimming with state-of-the-art technology that sheds light on biological context – essential to help you understand the big picture. The GGA produces results of higher relevance, answering your scientific questions with greater precision than ever before.

The biological background data consisting of annotation and gene network data provided by ElDorado plus the transcription factor knowledge contained in MatBase lets researchers analyze and interpret their experimental results in a unique biological context on every GGA for more than 30 different species. Differential expression analysis (down to the transcript level), network and pathway verification and generation, regulatory frameworks, literature analysis and binding site motif definition are only a few of the tasks that can be performed.

The GGA's award-winning intuitive web-based GUI is complemented by command line tools that can be integrated into workflows and pipelines, enabling users of all levels of experience to quickly and efficiently gain the scientific insight needed for applications or publications.

Together with the Genomatix Mining Station the Genomatix Genome Analyzer provides a complete analysis solution from raw sequencing tags to the biology behind your data. With seamless, convenient data transfer from the GMS to the GGA.

Key features

Key features of the Genomatix Genome Analyzer (GGA)

  • Offers the state-of-the-art technologies of the Genomatix Software Suite plus additional analysis capabilities for large data sets from Next Generation Sequencing experiments.
  • Provides first class genome annotation and background data for 31 species.
  • First fully integrated automatic ChIP-Seq data analysis workflow (classification and clustering of reads, sequence extraction, transcription factor analysis, automatic generation of binding site motifs and weight matrices from the data)
  • True second-level analysis that shows you the biology behind your data.
  • Use the same technologies that our in-house scientific consultants apply to customer projects.
  • Command line tools and direct annotation database access allow integration in your own workflows.
  • Not really a black box, as our algorithms have been published in peer-reviewed publications and the use of the software is documented in numerous scientific articles.

Technical data


Technical Data for the desktop version:
  • Description: The Genomatix Genome Analyzer desktop version consists of a Processing Unit and a RAID Storage System containing the hard disks in an external enclosure
  • Dimensions:
    Processing Unit: 430 x 155 x 360 mm (17 x 6.1 x 14.2 inches) (W x H x D),
    External RAID: 146 x 191 x 311 mm (5.8 x 7.5 x 12.3 inches) (W x H x D)
  • Weight:
    Processing Unit: 15 kg (33 lbs),
    External RAID: 9 kg (20 lbs)
  • Processor: 1 x QuadCore AMD Phenom 2 Processor
  • Memory:
    Internal: 16 GB RAM,
    Hard Disk space: 4 x 1TB HD (1TB for user data, 3 TB containing Genomatix' proprietary annotation data which will be replaced on updates)
  • Power Supply:
    Processing Unit: 100-240 V, 430 W,
    External RAID: 100-240 V, 180 W

Technical Data for the rack version:
  • Description: The Genomatix Genome Analyzer rack mount version consists of a 1U 19'' server enclosure with the hard disks built in.
  • Dimensions: 432 x 43 x 650 mm (17 x 1.7 x 25.6 inches) (W x H x D)
  • Weight: 19.5 kg (43 lbs)
  • Processor: 2 x DualCore or 1 x QuadCore AMD Opteron 2000 (additional cores available on request)
  • Memory:
    Internal: 16 GB RAM (additional RAM available on request),
    Hard Disk space: 4 x 1TB HD (1TB for user data, 3 TB containing Genomatix' proprietary annotation data which will be replaced on updates)
  • Power Supply: 100-240 V, redundant 650 W AC power supplies w/ PFC, 60-50 Hz, 8-4 amps

Release notes

Release notes of the September 2011 version

New and changed data

  • New genomes
    • Oryctolagus cuniculus (rabbit, NCBI build 1)
    • Xenopus tropicalis (western clawed frog, NCBI build 1)
  • Updated genomes
    • Arabidopsis thaliana (TAIR 10)
    • Bos taurus (NCBI build 5)
    • Danio rerio (NCBI build 4)
    • Sus scrofa (NCBI build 2)
  • Discontinued ElDorado versions:
    • ElDorado 07-2008
    • ElDorado 12-2008
  • Library Changes
    • Extended matrix library of transcription factor binding sites (Matrix Family Library Version 8.4):
      • Includes 43 new matrices (34 vertebrate, 9 plant).
      • Library contains now 1,326 matrices in 407 families.
    • Updated Restriction Site Library (based on REBASE version 107).
    • Extended Promoter Module Library (Module Library Version 5.5):
      • Includes 23 new vertebrate modules and 11 new plant module.
      • Library contains now 824 modules (738 vertebrate and 86 plant modules).
  • New data in MatBase
    • Based on the most recent matrix family library (Matrix Family Library Version 8.4).
    • Number of matches: the number of matches for each family/matrix in genomic and promoter sequences is given for all ElDorado species

New features of the Genomatix Software Suite (GGA version)

  • ElDorado
    • Completely new Genome Browser
      • Flash-based Genome Browser
      • User-friendly browsing of genomes and all annotations as available in the ElDorado database
      • Allows accessing a genome via position or going directly to a gene of interest
      • Intuitive view of locus complexity
      • Direct visualization of BED files (no need for preselecting "user data" in ElDorado)
      • Various display formats and export options
    • Transcriptome Viewer for alternative transcripts
      • Detection of new splice junctions by integrating splice junction mappings
  • RegionMiner
    • Replicates for ChIP-Seq-Workflow
      • allow merging clusters from different replicates (based on user parameters)
      • apply techniques for significance testing (DESeq or edgeR)
    • Peak calling in the Clustering-Task and ChIP-Seq-Workflow
      • included SICER as a third peak calling algorithm (recommended for histone modifications)
      • new MACS version 1.4.1
    • Large Scale SNP Analysis
      • added nucleotide coverage to output files
      • added distance to nearest splice site to output files
    • Upload of BED files from GGA/GMS
      • improved file chooser: now starts at the last location when used repeatedly
    • NE-values (normalized enrichment/expression values)
      • all NE values are now based on nucleotides instead of read numbers (to be more precise when reads do not fall completely into a region/transcript)
    • GenomeInspector:
      • added promoter ID / Symbol/ GeneID to the output of correlations with promoters
      • added the transcript quality to the output of correlations with transcripts
      • links to genomic positions now go directly to the Genomatix GenomeBrowser
    • RNA-Seq Expression Analysis
      • added data plots (fold-change/volcano) for Audic-Claverie results
      • links to GePS now open a new window
  • GePS
    • New shape for RNAs with gene IDs
    • Network extension for a single gene with all input genes
  • MatBase
    • TF verification: On the search page a list of gene ids or symbols can be entered which is then verified against MatBase. All search items matching a transcription factor are listed in the output table. A separate table contains the items that could not be verified.

New features of the Bioinformatics Workbench

  • New MACS version
    • version 1.4.1 is available alongside version 1.3.7
  • SNP Analyzer
    • added nucleotide coverage to output files
    • added distance to nearest splice site to output files
  • Replicate analysis
    • statistical methods for significance testing (DESeq and edgeR) available for ChIP-Seq clusters