Genome Trax: Variant Analysis
Watch a short video

BIOBASE Genome Trax™ is a comprehensive compilation of variant knowledge that allows you to quickly and confidently identify pathogenic variants in human whole genome or exome sequences.

If you are analyzing whole genome or exome sequencing data — Genome Trax™ is the tool to use. Genome Trax™ makes it easy to upload a complete genome’s worth of variations and, within an hour, identify the biologically relevant subset of known mutations, mutations that are novel and appear in a candidate disease genes, or mutations that are predicted to have a deleterious effect. The database includes the world’s most comprehensive collection of disease causing mutations from  HGMD® Professional and pharmacogenomics variants from PGMD™, as well as regulatory sites from TRANSFAC® , and disease genes, drug targets and pathways from PROTEOME™.  It integrates the best public data-sets on somatic mutations, allele frequencies and clinical variants, in their most up-to-date version, for a total of more than 165 million annotations.

Genome Trax™ provides a simple, easy-to-use online interface for biologists, geneticists and pathologists to find relevant variants within minutes, with no need for bioinformatics expertise.  You can identify known pathogenic variants, remove harmless common variants, and obtain deleterious predictions for novel variants.  If you have family data, you can identify variants that are de novo, compound heterozygous only in the offspring.  All of the results can be downloaded to Excel for further review.  For core facilities and bioinformaticians, the complete underlying data is made available for download and easy integration into custom analysis pipelines. Genome Trax™ data is already optimized to work with many other software packages, such as ANNOVARTM, CLC bio, Alamut, SimulConsult, and Cartagenia and is used by a large number of NGS service providers, researchers, pathologists and diagnostic labs.


  • Prioritize mutations from large-scale sequencing
  • Identify disease-causing mutations
  • Sequence genome of interest, reduce cost and time on trio comparisons
  • Reduce the amount of mutations you have to investigate
  • Identify novel mutations not previously reported in the literature
  • Predict if novel mutations are deleterious, result in protein changes or affect disease genes
  • Find diseases, drugs, and pathways linked to variants

Key Features

  • Positively identifies relevant variants, not just filtering
  • Fast turnaround time: whole genome analysis in under an hour, whole exome in minutes
  • Over 150,000,000 annotated features total
    • HGMD® Professional disease mutations and genes
    • Pharmacogenomic variants
    • TRANSFAC® gene regulatory elements: miRNAs, experimental transcription factor binding sites (TFBS), refined ENCODE ChIP-seq TFBS, refined ENCODE DNase hypersensitivity region TFBS, microsatellites, CpG islands
    • PROTEOMETM disease biomarkers, drug targets, pathway memberships
    • Up-to-date, unified access to annotation from dbSNP, COSMIC, GWAS catalogue, ClinVar
  • Integrated variant effect prediction for novel variants based on machine learning, conservation, allele frequency, effect on protein sequence, and curated functional annotation
  • Fully compatible with ANNOVAR, UCSC Genome Browser, Galaxy, CLC Genomics Workbench, Avadis NGS, Alamut®, GeneData, SimulConsult, Cartagenia BENCH, Microsoft Excel
  • VCF, tab-delimited, BED, UCSC, and Complete Genomics variant file format support


Access Options

An online subscription provides access to the Genome Trax web interface. Online subscriptions are available at the single named user, concurrent user, and institution-wide level. All subscription levels require IP plus username/password authentication.

A download subscription provides access to all Genome Trax annotations in the form of .bed and .gff formatted files and MySQL relational database dump. In this way, the complete Genome Trax data can be integrated into your own, or 3rd party, NGS analysis pipelines or tools. However redistribution of, or public access to / display of, the data is not allowed without prior written consent. A download subscription does not provide access to the Genome Trax web interface.

Click here for a table comparison of features available in online vs. download options.

Academic research user? Order now.
Commercial user/clinical, non-profit/academic service provider? Request a quote.