Avadis^® NGS

Genome Trax™, biological database, is accessible in Avadis NGS software to analyze RNA-Seq, DNA-Seq, and ChIP-Seq NGS data.  The integrated annotation tracks for human data (builds hg18 and hg19) are:

• 80,000+ disease linked mutations from HGMD® Professional
• 600,000+ ChIP-Seq fragments with best binding site predictions
• Post Translational Modifications (PTMs)
• Transcription Start Sites (TSSs)

Avadis NGS gives you the tools for identifying genomic variants in your NGS data. Annotating these variants with the superior, human curated annotations of Genome Trax will give you immediate insight into which of these variants is already known to be involved in a disease-related pathway or located in or near a known regulatory site. This knowledge will narrow down the regions of interest to your research, saving you valuable time and effort.

To learn more about the integration, or to request a live demo please contact us.

CLC Bio

The premiere software tool for visualizing and analyzing Next Generation Sequencing (NGS) data.  The combined solution of our user-friendly platform collection of eukaryotic gene regulation data and CLC bio’s cutting edge algorithms and can get you instant access to experimentally proven knowledge of genomics analyses.

Analyze NGS data faster than it is produced with cutting-edge technology and advanced algorithms in the Genomics Workbench NGS solution.

• Cross-platform desktop application with a graphical user-interface
• SIMD-accelerated assembly algorithm
• Supports and integrates with the rest of your typical NGS workflow
• Plug-ins available to expand your analysis capabilities with data types specific to your needs

Combine the advantages of TRANSFAC® with the CLC Bio Genomics Workbench

The TRANSFAC plug-in (or extension) can be used to analyze transcription factor binding sites in DNA sequences from your next generation sequencing data. Binding site predictions are made with the Match tool, using the positional weight matrix library from TRANSFAC. Each of these matrices contains optimized parameters, for minimization of error rates.

Request a quote or contact us.
Download a trial version or Download the TRANSFAC Plug-in

Interactive Biosoftware

Interactive Biosoftware’s application, Alamut®, expedites the mutation interpretation process in molecular genetics laboratories. It is based on first-class molecular biology databases and prediction methods, which are embedded in a rich and user-friendly graphical environment, to easily assess the effects of genomic variants.

Alamut also displays information from the Human Gene Mutation Database, available to HGMD® Professional subscribers. Users have an immediate access to HGMD variant and gene pages, as well as to PubMed citations.  Annotations from BIOBASE Genome Trax™ will also be available in a future version.

To learn more about the integration please contact us.

DNAnexus

Among the key features is a web-based and interactive Genome Browser with direct link-outs to content rich data sources, such as BIOBASE. The ability to link out to third party data sources, that contain relevant gene-to-disease knowledge, allows researchers for example to study how identified variations in DNA affect the response to diseases, bacteria, viruses, toxins and chemicals, including drugs and other therapies. Having access to that knowledge will help with the prioritization of a list of variants as well as the genes and processes impacted as a result of these variants.

For more information or to sign up for a free trial account, please contact DNAnexus.

Genedata

Genedata Expressionist for Genomic Profiling is a comprehensive, enterprise software solution that manages, analyzes, and visualizes massive amounts of next-generation sequencing data. Relied on by a significant number of researchers applying high-density analytical technologies, Genedata Expressionist integrates and analyzes genomics, transcriptomics, epigenetics, and phenotypic data within a single high-throughput system. Built on an open and flexible client-server architecture, the solution thrives on large experimental data sets from all major vendors and technology platforms and can be easily integrated into existing research IT environments. Genedata Expressionist allows for seamless integration of genomic annotation data from the Genome Trax™ database.

To learn more about the integration please contact us.

GenomeQuest

GenomeQuest is a global provider of large-scale genomic software applications.  Its flagship products are GQ-Research for management and analysis of genomic information at whole/multi-genome scale, GQ-Dx for decision support in whole-genome/exome/panel diagnostics, and GQ-IP for global research of genomic sequence intellectual property.

Researchers performing analysis using GQ-Reseach and GQ-Dx now have built-in access to HGMD, Biobase’s comprehensive database of mutation/binding site/disease genes.  In GenomeQuest, users identify variants, activate the HGMD tracks, and can then select, filter, and analyze in an enriched biological/medical context.  HGMD is available for purchase from GenomeQuest.