Genomatix Suite

Major features:

Additional new genomes annotated (now totaling 14 organisms)

  1. Danio rerio (Zebrafish)
  2. Apis mellifera (Honeybee)
  3. Caenorhabditis elegans (Nematode)

All annotations based on complete proprietary annotation pipeline. No gene predictions. Annotation purely by mapping of more than 530,000 transcripts and >16 million ESTs (EST display/tissue profiling available in the next release after this). Exhaustive cross-mapping with a superior proprietary algorithm of all transcripts between the different organisms leading to:

  1. Superior ortholog grouping in 25,116 homology groups with 3005 groups containing all vertebrates in ElDorado (homo, chimp, rat, mouse, zebrafish, chicken, dog, cow). No paralogs in the groups!
  2. New ultrafast algorithm for mapping sequences onto genomes
  3. Precise promoter annotation and prediction by multiple lines of evidence approach
  4. All single probes from Affymetrix GeneChip probe sets are annotated.


  • New Affymetrix chips incorporated, including the new Human Exon 1.0 ST array
  • Graphical display of identified transcripts and genomic region with single probe positions and significance
  • Presence/absence call for experiments without a control
  • Batch analysis feature for multiple analyses
  • Excel/Tab delimited file export of all underlying result data, transcript or single probe-based, for further external statistical analysis


  • New underlying technology to distinguish homonyms (by “right” and “wrong” context analysis)
  • Multi-column data upload
  • Range filter for expression values for each column

GEMS Launcher:

  • Identification of promoter frameworks with pre-defined mandatory elements in FrameWorker
  • Automatic permutation of alternative promoters for FrameWorker
  • Extended list comparison with values attached to list elements

Access Information:

Contact the NIH Help Desk: Telephone:

301-496-4357 (open 6:00 am – 6:00 pm).

Request Access: NCI at Your Service

GGA/GMS accounts: Genomatix Genome Analyzer and Genomatix Mining Station:

The Genomatix Genome Analyzer (GGA) is an integrated solution for comprehensive visualization and interpretation of Next Generation Sequencing (NGS) data from ChIP, RNA, DNA, methylation or small RNA sequencing.

It 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). A true second-level analysis that shows you the biology behind your data.

Command-line tools and direct annotation database access allow integration in your workflows.

You must submit a request through “NCI at Your Service” to obtain an account for access to all Genomatix software.


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