Genomatix GmbH
| File:Genomatix logo.png | |
| GmbH | |
| ISIN | 🆔 |
| Industry | Bioinformatics |
| Founded 📆 | 1997 |
| Founder 👔 | Dr. Thomas Werner |
| Headquarters 🏙️ | Munich, Germany |
Area served 🗺️ | |
| Members | |
Number of employees | |
| 🌐 Website | http://www.genomatix.de |
| 📇 Address | |
| 📞 telephone | |
Genomatix GmbH is a computational biology company headquartered in Munich, Germany, with a seat of business in Ann Arbor, Michigan, United States.
History[edit]
Genomatix was founded in 1997 by Dr. Thomas Werner as a spin-off from the Helmholtz Zentrum München (formerly "GSF, National German Research Institute for Environment and Health"). Helmholtz Zentrum Munich is part of the Helmholtz Association of German Research Centers.
Genomatix software tools[edit]
Genomatix offers technologies and databases for genome annotation and regulation analysis.
Genomatix's product portfolio contains products for:
• Literature and pathway mining
• Transcription factor analysis
• Genome annotation integrating a wide variety of transcript sources with a special focus on regulatory regions
• Analysis technology for high throughput genomic technologies (microarrays and next generation sequencing)
Literature mining
LitInspector is a literature search tool that provides gene and signal transduction pathway mining within NCBI's PubMed database.[1][2]
Pathway mining
GePS
BiblioSphere
Current research[edit]
Personalized medicine has developed into a major field for Genomatix.[3] Genomatix is involved in several projects and international conferences, including the fifth Santorini Conference, "Functional Genomics Towards Personalized Health Care."[4]
Since 2008, Genomatix has strongly focused on next-generation sequencing data analysis. Because of the large amount of data and the need for high-end computing power, Genomatix deploys its products as in-house installations (hardware and software bundles).
Two systems are available:
1. The Genomatix Mining Station (GMS) is based on a proprietary genomic pattern recognition paradigm, or GenomeThesaurus, which allows for the input of raw sequence reads, along with optional quality files from any deep sequencing hardware. It provides mapping of sequences of any length (starting from 8bp) with no practical limits on the number of point mutations and/or insertions and deletions that can be taken into account during the mapping process. Depending on the nature of the experiment, the GMS can provide SNP detection and genotyping, copy number analysis, and small RNA analysis. For ChIPseq data, the GMS performs clustering, peak finding, and automated binding pattern identification. For RNAseq experiments, normalized expression values are calculated at the exon and transcript levels. A special GenomeThesaurus is also provided for potential splice junctions, which allows for splice junction analysis and the identification of new transcriptional units.
For genomic re-sequencing and newly sequenced genomes, a de-novo assembly is provided.
2. The Genomatix Genome Analyzer (GGA) provides downstream software tools and databases for the deep biological analysis of data coming from the GMS. It allows for integration and visualization of the terabytes of background annotation in the ElDorado genome database. GGA extensively annotates genomic coordinates and surrounding areas derived by the GMS or other mapping procedures. Clustering and peak finding, analysis for phylogenetic conservation, large-scale correlation analysis with annotated genomic elements, meta-analysis of data correlation between different experiments, pathway mining for groups of identified genes, transcription factor binding site (TFBS) analysis (identification, over-representation, binding partner analysis, framework identification, phylogenetic conservation, regulatory SNP effects) can be carried out on the GGA.
References[edit]
- ↑ Frisch, M; Klocke, B; Haltmeier, M; Frech, K (2009). "LitInspector: literature and signal transduction pathway mining in PubMed abstracts". Nucleic Acids Res. 37 (Web Server issue): W135–40. doi:10.1093/nar/gkp303. PMC 2703902. PMID 19417065.
- ↑ [1] Archived 2019-05-11 at the Wayback Machine LitInspector start page.
- ↑ [2] Archived 2010-07-25 at the Wayback Machine Genomatix and personalized medicine.
- ↑ [3] Archived 2010-03-04 at the Wayback Machine Conference about personalized health care.
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