Genome Explorer

The BaseClear Genome Explorer is an online platform that provide users with interactive tools to easily analyse and visualize their microbial (meta)genomic 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 https://www.genome-explorer.com 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 info@baseclear.com for the option that best meet your needs.

ANALYSIS OF WHOLE GENOMES AND STRAIN COLLECTIONS

BROWSE AND VISUALIZE

The Genome Explorer provides an easy overview of your genomes. 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.

BASIC, ADVANCED AND BLAST SEARCH TOOLS

Search for specific genes, GC-contents and many other search parameters! The local BLAST search function gives the opportunity to BLAST a sequence of interest against one or more genomes (samples, projects or taxa). An advanced search tool allows automated queries on a number of parameters. Also the customer can limit the search to specific taxa or projects. Results can be exported in various formats.

COMPARATIVE GENOMICS

The Genome Explorer has two functions to compare genomes. The first allows to align multiple genomes using MUMer software (Kurtz et al. 2004) and compare these at a nucleotide level. The end result comprises interactive tables containing and overview of the aligned and unaligned regions as well as the predicted SNPs and Indels. The alignment is also displayed in a graphical manner.

The second allows to assess functional differences through the definition of the pan- and core genomes. This comparison is based on the presence or absence of orthologous groups within the different samples following the Roary approach of Seeman et al. 2015. The end result comprises a comprehensive table which can be dynamically adjusted to include or exclude samples. The table also allows to focus the analysis on specific genes of interest. Finally a tree is presented where the branches reflect the distances calculated from the presence/absence table.

REPORTS AND OVERVIEWS

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

Genome explorer reports and overviews

ANALYSIS OF METAGENOMES

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).

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DATA SECURITY

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.
BioInformatics data security

ADVANTAGES OF OUR GENOME EXPLORER

  • 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)
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