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: CLC Genomics Workbench

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.  To learn more about the integration please contact usDownload a trial version or Download the TRANSFAC Plug-in.

Comparative Genomics and Next Generation Sequencing (COGANGS)
The COGANGS project will develop a software suite, the COGANGS engine, where a large number of genomes can be used as knowledge input in gene regulation analysis.  Such software will be able to provide completely new knowledge, and will thus have tremendous value to life science researchers globally, including pharmaceutical companies, biotech companies, agricultural companies, biofuel companies, and research hospitals, as well as universities and governmental research organizations.


Interactive Biosoftware: Alamut / Alamut HT

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™ have been integrated into Alamut’s application.  To learn more about the integration please contact us.


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.


geneXplain

GeneXplain’s mission is to provide a comprehensive platform for bioinformatic, cheminformatic and systems biological tools. The raison d’être of this platform is to assist translational research in the life sciences, mainly in the context of personalized medicine and pharmacogenomics.  The geneXplain platform contains a number of modules (“bricks”) that seamlessly work with BIOBASE’s database TRANSFAC and with signal transduction content from BIOBASE’s PROTEOME database (“TRANSPATH”). One-stop shopping of the databases with the platform is possible.  To learn more about the integration please contact us.