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EMBL GeneCore purchases Genomatix's next generation sequencing data analysis solution

Genomatix Software, a leading provider of complete solutions for the analysis of Next Generation Sequencing (NGS) data, announced today that the European Molecular Biology Laboratory (EMBL) installed a Genomatix Mining Station and a Genomatix Genome Analyzer at its Genomics Core Facility. These systems deliver the only complete and integrated analysis solution for NGS data, from the raw data generated by the sequencer, to a molecular level understanding of the biology being studied.

"Based on joint scientific approaches and collaborations, it is clear that we have a long term relationship with Genomatix. As such, we have received early access to their solution for NGS data analysis," says Dr. Vladimir Benes, Head of Genomics Core Facility at EMBL. "We did thorough tests with real life data sets and were impressed by the speed, ease of use and extended reach into the biology provided by their system. The amount of high quality data being produced at our core facility every day necessitates analysis pipelines that can keep pace."

Klaus May, Chief Business Officer at Genomatix says: "We are very pleased that the EMBL has chosen our GMS and GGA. With our combined hardware/software approach, we are prepared for the arrival of the data tsunami expected from Third Generation Sequencers and beyond. For EMBL, with brilliant scientists from all fields, ease of use was important so that the biologists can readily use the system through it's easy to use graphical interface. The bio-informaticians were equally pleased to find that they could approach the extensive software and data content with command line access. "

The Genomatix Mining Station (GMS) is based on a proprietary genomic pattern recognition paradigm, or GenomeThesaurus, which allows for input of raw sequence reads plus optional quality files from any deep sequencing hardware. It provides ultra fast mapping of sequences of any length (starting from 8 bp) 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 delivers clustering and peak finding, and performs automated binding pattern identification. For RNAseq experiments, normalized expression values are calculated at the exon and transcript level. A special GenomeThesaurus is also provided for potential splice junctions, which allows for splice junction analysis and identification of new transcriptional units.

For genomic re-sequencing and newly sequenced genomes, a de novo assembly will be provided.

The Genomatix Genome Analyzer (GGA) delivers downstream software tools and databases for the deep biological analysis of data coming from the GMS. It allows for easy integration and visualization in the terabytes of background annotation of the ElDorado genome database. GGA extensively annotates genomic coordinates and surrounding areas derived by the GMS or any other mapping procedure. 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) and much more are all processes carried out on the GGA.

EMBL's Genomics Core Facility (GeneCore) is the in-house genomics service centre at EMBL equipped with state-of-the-art technologies required for functional genomics analyses and operated by highly-qualified staff. The focus is on the benefits and utilization of new technologies, which are also developed at EMBL, to improve the quality, efficiency and relevance of laboratory data.


Contact: Klaus May
Genomatix Software GmbH

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