Genomatix GGA and GMS

Category Cross-Omics>Next Generation Sequence Analysis/Tools

Abstract Genomatix Genome Analyzer (GGA) and Genomatix Mapping Station (GMS) are integrated hardware/software solutions for in-depth analysis of data generated by next generation sequencing (NGS) devices.

Genomatix Genome Analyzer (GGA) -- Used to analyze your NGS data using Genomatix' comprehensive software tools.

Genomatix Mapping Station (GMS) -- Provides genome positioning, splice analysis and genotyping using the data from your NGS experiment (see below).

Genomatix Genome Analyzer --

1) Extract the relevant biological knowledge from Chromatin immunoprecipitation-Sequencing (ChIP-Seq) and Digital Gene Expression (DGE) studies.

2) Correlate and visualize NGS results with an extended genome annotation.

3) All required data and hardware in one technology unit at your site.

Satisfies all needs of a modern research environment -

1) Full data structure access and command line driven procedures for the bio-informatician.

2) Comprehensive easy-to-use web based interface for the biologist.

3) Full integration into existing pipelines and network environment.

Provides a genome wide correlation with annotation -

1) Clustering of mapped sequence reads.

2) Integration and visualization in today's most complete genome annotation (ElDorado™ another advanced product from this manufacturer).

3) Genome wide correlation with all available genomic features - includes transcripts, Single Nucleotide Polymorphisms (SNPs), scaffold/matrix attachment regions (S/MARs), CAGE tags, transcription start sites (TSSs), untranslated regions (UTRs), CDSs, microRNAs, repeats.

4) Identification of phylogenetically conserved functional elements.

5) Data meta-analysis.

Provides a complete analysis for ChIP-Seq experiments -

1) Classification of clusters (promoter, exon, intron, intergenic).

2) Genome-wide chromatin modification and methylation state analysis.

3) Genome-wide transcription factor (TF) analysis.

4) Analysis of TF overrepresentation and TF association.

5) Regulatory SNP analysis.

6) Cross-Species analysis for phylogenetically conserved regions and regulatory structures.

Provides a complete analysis for transcriptome studies -

1) Normalized expression values.

2) Quantification of expression values.

3) Identification of new transcriptional units and splice variations.

4) Visualization of transcriptional units with exon/intron structure, UTRs, CDSs.

Provides statistical analysis of over-represented transcription factor binding sites - Genomatix' MatInspector™ software (see G6G Abstract Number 20229) can be applied to find the most relevant regulatory elements for your experiment (e.g. in significantly enriched regions derived by ChIP-seq of the estrogen receptor - output can be exported to Excel™).

Provides genome-wide correlation with genomic features - Quickly check your data for distance correlations to transcription start sites, promoter regions, microRNAs or against another data set from your lab (e.g. Correlation of histone methylation (H3K4me3) enriched regions from ChIP-seq vs. transcriptional start regions or DNase I tags vs. promoter regions).

Provides integration and visualization in today's most complete genome annotation - Cluster your sequence reads and instantly view them in their genomic context within Genomatix' extensive genome annotation package ElDorado™ (e.g. DNase I sequence reads near the gene "RARA" on human chromosome 17).

Genomatix Mapping Station (GMS) - The Next Generation in Mapping Technology --

An ultra high speed solution for - Genomic positioning; Genotyping; and Splice analysis.

The Genomatix Mapping Station Delivers -

1) Genomic positioning: Read mapping; Low frequency copies; Alignments; General statistics; Quality reporting; Point mutation and insertion or deletion (Indel) classification.

2) Genotyping (see Note below): Advanced de-novo SNP detection; Correlation with known SNPs; Haplotype analysis; Differential Genotyping; Copy number variations;

3) Splice analysis: Splice junction identification and Splice indices.

Proprietary GenomeThesaurus™ genomic pattern database technology delivers regional information content for each genomic / transcriptomic position and gives comprehensive information for each sequence read -

1) Unlimited read length starting from 8 bases.

2) No algorithmic limit on number of point mutations and insertions and deletions.

3) Advanced handling of repetitive reads.

4) Support of sequence space as well as color space.

5) Mapping speed of up to 1 million bases per minute to the human genome.

6) Accepts and considers sequencing quality information optionally.

7) Dedicated special purpose built hardware with UNIX operating system.

Supports all Next Generation Sequencing platforms:

1) SOLiD™ System by Applied Biosystems™.

2) Genome Sequencer™ by 454 Life Sciences™ (a Roche Company).

3) Genome Analyzer by Illumina™.

4) HeliScope™ by Helicos™.

Note: Genotyping is an upcoming feature of Genomatix Mapping Station and might Not be available on early release versions of the product.

System Requirements

Contact manufacturer.

Manufacturer

Manufacturer Web Site Genomatix GGA and GMS

Price Contact manufacturer.

G6G Abstract Number 20278

G6G Manufacturer Number 101114