Online ordering
Login Register


The BaseClear Genome Explorer is an online platform that provide users with interactive tools to easily analyze and visualize their microbial (meta)genome data. The system comprises a number of modules that focus on a rapid functional interpretation of single genomes, strain collections and metagenomic communities. The input consists of assembled and annotated genomes in GenBank format or taxonomy (OTU) tables in the case of communities. We also accept sequence data that have been generated at an external provider or are retrieved from (public) databases such as the NCBI. At present the platform comprises the following features: 

  • Genome browser to interactively visualize whole genomes
  • Genome mining tool to screen genomes using queries or BLAST function
  • Genome comparison through the whole genome alignment or gene comparisons (based on orthologous groups)
  • Antibiotic resistance to assess the safety of strains
  • Microbial profiling to perform multilevel taxonomic analysis accross samples  

The Genome Explorer is accessible via and supported for Firefox, Internet Explorer (version 9 and higher) and Chrome. The system is protected using the latest standards which are further detailed below. 

Licenses are available upon request, please contact us at for the option that best meet your needs. 



Browse through your projects and samples using our comprehensive overview pages (project-based and taxonomy-based). Visualize genes and genome structures using our graphical interface.

The Genome Explorer provides an easy overview of of your genomes. Also a graphical interface is available to view genes and genome structures. Results can be exported in various formats.


Search for specific genes, GC-contents and many other search parameters! Also a local BLAST approach is available to allow the search of particular sequences.

An advanced search tool allows automated queries on a number of parameters. Also the customer can limit the search to specific taxa or projects.

The local BLAST search function gives the opportunity to BLAST a sequence of interest against one or more genomes (samples, projects or taxa). Results can be exported in various formats. 


The Genome Explorer has two outstanding functions to compare genomes. The first is included in the standard software package and allows to align multiple genomes and compare these at a nucleotide level. Also a mutation analysis is included to give you the full picture of variations between the selected organisms.

The Genome Explorer has a unique function to compare multiple genomes at a nucleotide level. Not only a graphical overview is available, also a table with corresponding sequences and genes is provided which can be dynamically inspected using queries (e.g. on specific gene names or clusters). 

Furthermore the Genome Explorer has a new option to compare (many) genomes based on the absence or presence of orthologous groups. The prediction of the orthologous groups is performed offline by our Bioinformatics experts and requires an additional analysis fee. Yet the results are easily interpretable in the Genome Explorer: the interactive Pivot table in combination with the phylogenetic tree provide direct insight into the functional differences between strains and the definition of a core-genome. 

The Genome Explorer has a also an option compare multiple genomes based on the presence or absence of orthologous groups. The resulting Pivot table displayed here can be also combined with meta-data thus allowing an easy connection between functional and phenotypic data.


The Genome Explorer offers the unique feature to easily generate reports with an overview of several statistics, and for instance also predicted enzyme classes.



At present the system is developed for visualization of 16S or ITS-based targeted sequence analysis, but will be extended also for whole-metagenome analysis in the near future. In brief the online portal allows interactive inspection of taxonomy tables and associated trees, but also provides comprehensive overviews in pie chart and bar charts. The user can specify the desired taxonomic level (e.g. genus or species) and has also the possibility to export all corresponding analysis tables and figures. Finally the system includes a feature for species-diversity analysis (alpha-diversity).






The Genome Explorer is hosted in the Microsoft Azure cloud. To guarantee data security the following measures have been taken: 

  • Physical infrastructure security – the necessary servers for the cloud infrastructure are deployed in regional datacenters within Europe (the European Economic Area (EEA))
  • Cloud infrastructure security – security measures are always compliant to ISO/IEC 27001; Servers, networks, and applications are continuously monitored to detect threats. Access control and traffic flow policies apply to prevent unauthorized and unintentional transfer of information.
  • Genome Explorer Infrastructure security - Industry-standard protocols are used to encrypt data in transit, communication between the Genome Explorer infrastructure and on-premises resources is tunneled trough a VPN which uses numerous encryption mechanisms, including SSL/TLS, IPsec, HMAC-SHA1/SHA2, TripleDES-CBC, AES-CBC and, AED-GCM. Data nodes are not accessible from the public internet.



  • Fast interpretations and conclusions, easy to share results with your team
  • Optimal usage of the Microsoft Azure cloud infrastructure
  • Compliance with ISO27001 and other leading information security standards 
  • Easy and fast screening of multiple samples and strain collections (up to 10.000 samples)
  • Advanced search/query functions including local BLAST 
  • Additional modules for Genome comparison and Strain characterization (including antibiotics resistance assessment)
  • Dedicated module available for analysis of bacterial and fungal communities based on OTU profiling
  • Multiple options for export of results (i.e. figures, tables, etc.)
  • Publication-ready figures including circular alignment plots
  • Cost-aware pricing model with sharply priced subscription model
  • No installation of software needed
  • Online portals are supported by all main Internet browser (Firefox, Internet Explorer (version 9 and higher) and Chrome)
  • Possibility to customize the online portal to meet your specific needs, in-house bioinformaticians are available to provide a fast implementation
  • Possibility to connect upload other genomes (e.g. GenBank) and/or connect with genome databases (e.g. NCBI genomes)

Meet Walter Pirovano!

Walter is director of the bioinformatics department and supervises our team of excellent bioinformaticians with expertise in the field of next-gen analysis and (far) beyond.

Testimonial DuPont Industrial Biosciences

The support that BaseClear has provided in the field of bioinformatics and downstream processing of next generation sequencing data has been extremely important for us. There are of course other organisations that offer next generation sequencing but that does not mean that you have everything you need. BaseClear's extra service is unique and represents one of their great strengths.

Senior Scientist


Get a quote Meet Baseclear Contact form