Microbial Genome Annotation & Analysis Platform

Logo The Quality Management System of the LABGeM team has been certified according to the ISO 9001:2015 and NF X50-900:2016 standards (Lloyd's Register Quality Assurance France S.A.S.). The certification applies to LABGEM activities of research, developments, services and MicroScope trainings.

What is the MicroScope platform?

Located at Genoscope (the French National Sequencing Center), the LABGeM bioinformatics team has developed MicroScope (Vallenet et al., 2006, 2009, 2013) which is a web-based platform for microbial comparative genome analysis and manual functional annotation.

Its relational database schema 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 data needed for assigning the best possible annotation to a given gene product. These data are:

  • sequence-based (e.g., InterPro domain predictions),
  • context-based (i.e., synteny results and metabolic network predictions),
  • experimental (e.g., growth experiments, if any),

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.

What type of projects can be handled in MicroScope?
(re)Annotation and comparative analyses of finished or draft genome sequences.
Annotation and comparative analyses of metagenomic sequences. Currently, we are able to integrate datasets below 20 Mb.
RNA-Seq analysis
Map a RNA-Seq dataset to a reference genome and perform differential expression analyses.
Variant profiling
SNP/indels detection among different evolved strains by comparison with a reference genome.
How to integrate your own data into MicroScope?
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