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MicroScope
Microbial Genome Annotation & Analysis Platform

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?

Genome BrowserGet an overview of MicroScope and its current projects?
676 Available Organisms



103 Available Projects




Genome BrowserReferences
RSS Latest News

MicroScope platform: v2.4.0 deployed
Posted on: Thursday 19 January 2012


The v2.4.0 of the platform is now deployed:

- «RNASeq Projects - Overview» tool now allows to download coverage files in .wig format (more info).

Please report us any bugs you may meet.


MicroScope platform: v2.3.9 updated
Posted on: Wednesday 18 January 2012


The v2.3.9 of the platform is updated:

- A «Guest Book» webpage is now available on the platform.
- Information about MicroScope professionnal trainings is now available on the homepage.

Please report us any bugs you may meet.


MicroScope: Professional Training - February 7th 2012 to February 10th 2012
Posted on: Thursday 5 January 2012


A Training Course on the MicroScope platform will be organized at the INSTN Center of Saclay from Tuesday 7th of February to Friday 10th of February 2012.

-  Get more information about «Annotation and analysis of prokaryotic genomes using the MicroScope platform» training course.
-  Click here for the training course registration form.