Training «Annotation & Analysis of Prokaryotic Genomes using the MicroScope Platform»

In an effort to inform members of the research community about our annotation methods, to provide training for collaborators and other scientists who use the MicroScope platfom, and to inform scientific public on the analysis available in PkGDB (Prokaryotic Genome DataBase), we have developed a 4.5-day course in Microbial Genome Annotation and Comparative Analysis using the MaGe graphical interfaces.

This course will familiarize attendees with LABGeM’s annotation pipeline and the manual annotation software MaGe (Magnifying Genome) . No specific bioinformatics skill is required: detailed instruction on the algorithm developed in each annotation methods can be found in specific training courses on «Genomic sequences analysis». Here we focus on the general idea behind each method and, above all, the way you can interpret the corresponding results and combine them with other evidences in order to change or correct the current automatic functional annotation of a given gene, if necessary.

This course will also describe how to perform effective searches and analysis of procaryotic data using the graphical functionalities of the MaGe’s interfaces. Because of the numerous pre-computation available in our system (results of “common” annotation tools, synteny with all complete bacterial genomes, metabolic pathway reconstruction, fusion/fission events, genomic islands, …), many practical exercises allow attendees to get familiar with the use the MaGe graphical interfaces in order to efficiently explore these sets of results. 


Annotation and comparative analysis of bacterial genomes:

  • acquire theoretical and practical knowledge of genome annotation tools (structural and functional annotation, metabolic networks annotation)
  • interpret the results of functional annotation tools
  • perform various comparative analyses : conserved synteny analyses, pan-genome, phylogenetic and metabolic profiles.
  • analyse the results of metabolic networks prediction tools and look for candidate genes for enzyme activities.
  • use the tools to analyse the genome(s) of interest of participants


  • Engineers, researchers, experienced technicians from biological or medical research laboratories.
  • Pre-requisite: basic level in biology and computer skills.
  • Maximum number of trainees: 12


Introduction to genome annotation

  • Sequencing and annotation of microbial genomes
  • Introduction to the MicroScope platform

Syntactic and functional annotation

  • Gene prediction
  • Similarity analyses using various public databases
  • Prediction and usage of synteny groups
  • Prediction of enzymatic functions

Expert annotation

  • Using the results of the different methods to improve annotation
  • Annotating pseudogenes and fragments

Comparative genomics

  • Synteny and phylogenetic profiles
  • Region of genomic plasticity analysis
  • Core/pan genome analyses

Bacterial metabolism :

  • Databases on metabolism
  • Reconstruction of metabolic networks
  • Annotation and comparative analysis of metabolic pathways


  • Lectures (50%) and hands-on (50%). 
  • Each lecture is followed by computer-based exercises using the MicroScope bioinformatic platform.
  • Evaluation of the trainees is done during the hands-on sessions.
  • Training course and documents provided in english


  • Length: 4.5 days
  • Timetable: 9H-17H30
  • Location: Université d’Evry-Val-d’EssonneAccess.


Price (excludes VAT): 1350,00€ for academics, 2500,00€ for private companies 
Special offer for students, in the limit of available seats: 945,00€ 


Please see the Upcoming Sessions and fill the form of the chosen training course and click on Register. 

Our collaborators, from the Evry University, in charge of the training course organization will contact you for the administrative process in order to receive the detailed estimate, as well as the training agreement. 

Registrations will be closed 1 month before the beginning of the training course (subject to a sufficient number of registrations). 

Training courses will be maintained if there’s at least 7 attendees. 


Information – Registration 
Tel : +33 (0)1 69 47 70 67 
Fax : +33 (0)1 69 47 71 05 
Email :

Information – Training Course 
Alexandra CALTEAU 
Tel : +33 (0)1 60 87 84 57 
Fax : +33 (0)1 60 87 25 14 
Email :