The MicroScope platform is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Starting from the results of our syntactic, functional and relational annotation pipelines, MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic genomes. It combines tools and graphical interfaces to analyze genomes and to perform the manual curation of gene function in a comparative genomics and metabolic context. The resource provides data from completed and ongoing genome projects together with post-genomic experiments (i.e. transcriptomics, re-sequencing of evolved strains, mutant collections) allowing users to improve the understanding of gene functions.
The MicroScope platform is constantly evolving both in terms of data content and of new analysis tools some of them being developed in the context of our research projects.
Last news about MicroScope:
The version v3.14.3 of the platform is now deployed: The Access Rights Managment page now uses the new genome selector.A bug prevented SwissProt/TrEMBL annotations to be displayed on the gene info page. This is now corrected.Links to the PPanGGoLiN tool (used on the Regions of Genomic Plasticity - PanRGP page) ...Read More
MicroScope services (integration of new genomic data) will be closed from December 19th 2020 to January 4th 2021. User support will also be very limited during this period. The LABGeM team wishes you a happy holiday season ...Read More
Since 2004, MicroScope has offered a genome analysis service to a large community of microbiologists. The current resources of MicroScope are largely provided by the CEA and the CNRS through the funding of permanent staff and IT resources with the support of the French Institute of Bioinformatics of which the ...Read More
After the cancellation of 2020 trainings due to the Covid-19 crisis, we are pleased to inform you about MicroScope professional training courses in 2021. Two sessions of the «Annotation and analysis of prokaryotic genomes using the MicroScope platform» course are planned at the University of Evry: Monday 15th March 2021 ...Read More
This year, we worked on improving the genome integration request service. The main new functionality is that the request to update the assembly of a genome, previously transmitted by e-mail, can now be made online using the Delivery of Service Management page in the User Panel menu. We also fixed ...Read More
Two novel interactive graphs have been added to the RNA-seq analysis page to summarize, control and explore more deeply the Differentially Expressed Gene (DEG) results. A colored horizontal bar chart displays global statistics for the selected comparison(s).A MA-plot displays an overview of the results by plotting the log fold change ...Read More
The version 3.14.2 of the platform is now deployed: A new method for the prediction of KO numbers based on KofamScan has been integrated. Read more here. Note that this method allows the prediction of EC numbers. Therefore, the prediction of EC numbers based on PRIAM will be soon removed.There ...Read More
Two unrelated bugs have recently been fixed concerning BLAST results. The first was missing results in some workflows (e.g. Virulome). This concerned very few results when identical HSPs were detected. The second one affected the output of the BLAST search server: some results were missing when multiple HSPs were detected ...Read More
The v3.14.1 of the platform is now deployed: The features (starts, compositional features) and experimental data (gene essentiality, SNP, In/Dels, etc.) of a Genomic Object are now presented in a dedicated section in the Gene Annotation window (instead of being mixed with the results of annotation methods). See here for ...Read More
The v3.14.0 of the platform is now deployed: The main new functionality is that the request to update your genomes, previously transmitted by email, can now be made online via the Delivery of Service Management page in your user panel. Another interesting new feature is the addition of interactive MA-plot ...Read More