Genomatix Mining Station (GMS)
|
Application data |
|
| Created by | Genomatix Software |
|---|---|
| Biological application domain(s) | RNA-Seq, SNP detection, ChIP-seq |
| Principal bioinformatics method(s) | Sequence assembly, Read mapping, SNP calling, Correlation |
| Technology | Illumina, ABI SOLiD, Helicos, 454 |
| Created at | www.genomatix.de |
| Maintained? | Yes |
| Input format(s) | solexa, Solexa with Probability, FASTA, FASTQ, EMBL, GenBank |
| Output format(s) | FASTA, BED, SAM, BAM, GAF |
| Software features | Client-server based system allows for command-line and web-based access. Grid engine is used for job scheduling and mapping is run on multiple cores. Can be combined with a Genomatix Genome Analyzer (GGA) for a fully integrated NGS solution. |
| Programming language(s) | C++, Java, Flash |
| Licence | Commercial |
| Operating system(s) | Windows, Mac OS X, Linux |
Summary: The Genomatix Mining Station (GMS) offers mapping of NGS reads onto genomes, transcriptomes and splice-junction libraries. It is a client-server based solution and can be controlled through an intuitive GUI or via command-line. It covers different tasks such as, as genomic positioning, SNP detection, splice analyses and genomic enrichments. 200px|right
"Error: no local variable "counter" was set." is not a number.
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 solutions as in-house installations (hardware software bundle)
Two systems are available:
- 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 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 ChIP-seq data, the combined GMS/GGA solution 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.
- 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.
With the GGA and GMS Genomatix delivers the worldwide first integrative data analysis platform for Next Generation Sequencing analysis with custom workflows tailored towards specific needs. Further developments will be the link-up of data from clinical sources and medical applications. Pilot projects were already started within Genomatix’ consulting platform linking genotype and phenotype information.
Links
References
none specified
To add a reference for Genomatix Mining Station (GMS), enter the PubMed ID in the field below and click 'Add'.
Search for "Genomatix Mining Station (GMS)" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
