See the biology behind the data.

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.

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 GGA:
  • Description: The Genomatix Genome Analyzer consists of a 2U 19'' server enclosure with the hard disks built in.
  • Dimensions: 437 x 43 x 716 mm (17.2 x 1.7 x 28.2 inches) (W x H x D)
  • Weight: 31.3 kg (69 lbs)
  • Processor: 4 x 8Core AMD Opteron
  • Memory: 128 GB RAM, Hard Disk space:
  • Hard disk space: 4 x 4TB HD RAID for user data (accessible space: 12TB) , 2 x 4TB HD containing Genomatix' proprietary annotation data which will be replaced on updates)
  • Power Supply: 100-240 V, redundant 1400 W AC power supplies w/ PFC, 50-60 Hz, 15 amps max

Release notes

Release notes of the July 2015 version

Data background

  • 8 updated genomes, including human (GRCh38), and new transcript annotation for all 33 organisms within the ElDorado™ database
  • Extended matrix library of transcription factor binding sites (MatBase Version 9.3):
    • Includes 4 new vertebrate matrices
    • Library now contains 1,578 matrices in 444 families
  • Updated Restriction Site Library (based on REBASE version 506)
  • More than 200 new transcription factor binding site tracks in GenomeBrowser
  • Extended Promoter Module Library (Module Library Version 5.9):
    • Includes 16 new vertebrate modules
    • Library now contains 950 modules (851 vertebrate, 98 plant, 1 fungi)
  • Literature data update, now based on PubMed, 05-2015
  • Homo sapiens NCBI build 36 / hg18 will no longer be supported. Discontinued ElDorado versions are
    • ElDorado 07-2009 (including Homo sapiens NCBI build 36 / hg18)
    • ElDorado 02-2010
    • ElDorado 12-2010

New features of the Genomatix Software Suite (GGA version)

  1. NGS Analysis:

    • New task: Structural Variant Detection
      Note: This task is only available on GGA hardware with more than 16GB main memory
    • New task: Principal Component Analysis for Replicate Analysis
    • MicroRNA Analysis can automatically run a PCA on the input files
  2. Genes & Genomes:

    • ElDorado: improved sequence search in genomes based on BLAST
  3. Gene Regulation:

    • Matrix definition: Sequence logos can be downloaded in various formats (e.g. for publication)
  4. Literature & Pathways:

    • LitInspector and GePS are now based on the latest Literature (05-2015)
    • LitInspector, Release 1.8: Tagging of Diseases, Tissues, and Small Molecules now based on the UMLS database
    • Gene-TF-Analysis
      • Added direct links to co-citations
      • Added input options (input can be various keywords like GeneIds, accession numbers, symbols)
    • GePS (Genomatix Pathway System)
      • new graphical representation for regulations
      • Export: added support for graphics in 'TIFF' and 'EPS' format
    • GeneRanker
      • new annotation type Clinical Diseases, based on ClinVar
      • annotation type "Small Molecules (Genomatix Literature Mining)" replaced by "Pharmacological Substances (Genomatix Literature Mining)"
      • annotation types "Associated Cancer Tissues (COSMIC)" and "Chemical Entities of Biological Interest (ChEBI)" are discontinued
  5. Genomatix Tools:

    • BAM file tools: extended BAM file statistics with
      • more information on reads in BAM file (flags like paired, unpaired, mapped etc are shown)
      • graphics for chromosome distribution
      • optional classification of input reads on exons, introns, promoters or intergenic