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MicroScope
Microbial Genome Annotation & Analysis Platform

Logo The Quality Management System of the LABGeM team has been certified according the ISO 9001:2008 standard in january 2012 (Lloyd's Register Quality Assurance France S.A.S.).


Located at Genoscope (the French National Sequencing Center), the LABGeM bioinformatics team has developed MicroScope (Vallenet et al., 2006, 2009) which is a web-based platform for microbial comparative genome analysis and manual functional annotation.

Its relational database schema (PkGDB, for «Prokaryotic Genome DataBase») stores precalculated results of syntactic and functional annotation pipelines as well as Pathway Tools metabolic analysis specific to each genome. PkGDB is also linked to these metabolic pathway databases (MicroCyc). The MicroScope web interface (MaGe, for «Magnifying Genomes») has been specifically designed to assist curators in the evaluation of all available sequence-based (e.g., InterPro domain predictions), context-based (i.e., synteny results and metabolic network predictions) and experimental data (e.g., growth experiments, if any), with the aim of assigning the best possible annotation to a given gene product.

Moreover, MicroScope offers many useful data-exploring functionalities, such as allowing users to perform (complex) queries, comparative genomic studies, and metabolic analyses. It also provides summary views of statistics and information for each genome as a whole. Finally, MicroScope can be used both as:
  • a community resource, for comparative analysis and annotation of publicly available genomes
  • a private resource, as access rights to private projects can be restricted to a limited group of annotators defined by the project leader.
In addition, the LABGeM organizes regularly some professional trainings sessions about the use of MicroScope platform. General information and upcoming sessions are available on LABGeM's website.

Genome BrowserWhat type of projects can be handled in MicroScope?
  • Genome project: (re)Annotation and comparative analyses of finished or draft genome sequences.
  • Metagenome project: Annotation and comparative analyses of metagenomic sequences. Currently, we are able to integrate datasets down to 20 Mb.
  • RNAseq project: Map a RNAseq dataset to a reference genome and perform differential expression analyses.
  • Evolution project: SNP/indels detection among different evolved strains by comparison with a reference genome.
Genome BrowserHow to integrate your own sequences into the MicroScope web platform?
  • Take advantage of additional features.
  • Stay informed about new organisms releases and LABGeM communications.
  • Participate to user surveys.
Genome BrowserGet an overview of MicroScope and its current projects?
742 Available Organisms



108 Available Projects



Genome BrowserReferences
RSS Latest News

MicroScope platform: v2.4.4 deployed
Posted on: Friday 13 April 2012


The v2.4.4 of the platform is now deployed:

-  Gene Editor now integrates a «Rhea Reaction» editable field.
-  Get more information about Rhea

Please report us any bugs you may meet.

MicroScope platform: v2.4.2 deployed
Posted on: Friday 23 March 2012


The v2.4.2 of the platform is now deployed:

It is now possible to curate the MicroCyc pathway prediction for a given organism using the «Pathway Curation» tool.

Please report us any bugs you may meet.

MicroScope platform: v2.4.1 deployed
Posted on: Tuesday 21 February 2012


The v2.4.1 of the platform is now deployed:

- It is now possible to automatically proceed to account registrations. This is the first step for a future «Service Management System» dedicated to project leaders. New functionalities will be added as work proceeds.
- Project leaders can now dynamically and directly update their collaborator’s access rights to sequences by using the «Account & Right Management» interface.
- Users can now get contigs/scaffolds sequences from the «Genome Overview» interface.
- Due to Javascript library and CSS updates, please clear your browser cache.

Please report us any bugs you may meet.

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