Genomatix and Next Generation Sequencing

With the emergence of the "Next Generation Sequencing" (NGS) technologies such as Roche/454 Life Sciences™, Illumina/Solexa™ Sequencing and AppliedBiosystems SOLiD™, sequencing costs are brought down by several orders of magnitude, making the analysis of defined biological experiments feasible.

Genomatix is a company with a renowned track record in the analysis of genomic data generated by high throughput technologies. One focus is on overlaying experimental data with biological knowledge collected by sequence analysis, literature data mining, extensive genome annotation and transcriptional regulation analysis. Algorithms developed by Genomatix include optimized fast mapping strategies as well as pattern recognition procedures.

Genomatix has completed a number of pilot studies in collaboration with customers, successfully analyzing NGS data. Based on these projects considerable insights into the biological processes under study were obtained, providing additional information about the transcriptome and its regulation.

Genomatix' capabilities in Digital Gene Expression (DGE) studies:

• High efficiency mapping of raw sequence tags
• Data integration into up-to-date genome annotation and visualization
• Correlation with genomic elements (transcriptional start regions, promoters, S/MARs, intron/exon structures and more)
• Detection of tissue and cell specific transcription
• Definition of new transcriptional units
• Detection of new splice variants by complete transcriptome mapping; special focus on splice junction tags extending the exon/intron boundary

Special features for ChIP Sequencing (ChIPSeq) assays:

• Elucidation of active regulatory regions, both known and previously undescribed (e.g. enhancers)
• Genome wide chromatin modifications and methylation states
• Genome wide detection of TFs
• Phylogenetic conservation of regulatory regions (including enhancers)
• Downstream transcription factor (TF) analysis, TF overrepresentation, TF patterns, cooperative binding of TFs
• TF pattern discovery of yet undescribed binding motifs
• Elucidation of co-regulation mechanisms by overlaying DGE data

Genomatix is ready to provide services for NGS studies within our consulting model. If you are interested in hiring our analysis services and biological consulting for this kind of data, please send an email to research@genomatix.de or contact us and we will find a solution tailored to your needs.

-> See the example data "genome wide open chromatin" from an Illumina Solexa run here!