MicroScope platform

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:

MicroScope platform: v3.15.2 released

The version 3.15.2 of the platform is now deployed: The DBCAN workflow has been updated to use dbCAN v2.MicroScope now includes some metadata from a recent article (see Joshua S. Madin et al., A synthesis of bacterial and archaeal phenotypic trait data. Sci Data 7, 170 (2020)). More precisely, we ...
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Important changes in MicroScope data management

In order to optimize data management in MicroScope we have decided to proceed to several changes. First we have decided to remove obsolete genome assemblies from MicroScope. This step concerns genomes from GenBank which have been deleted from the database (see the list here). If you need these genomes for ...
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MicroScope platform: version 3.15.1 released

The version 3.15.1 of the platform is now deployed: In this version, we introduced management of deleted synteny results for genomes that are no longer consulted. More on this soon. We also fixed various bugs. Please report us any bugs you may meet ...
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MicroScope platform: v3.15.0 released

The version v3.15.0 of the platform is now deployed. The main novelty in this version is that we now use KEGG Orthology (KO) computed by KOfamScan to map genes to EC numbers and KEGG pathways instead of PRIAM results (see the documentation here). PRIAM results are no longer available in ...
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MicroScope platform: v3.14.3 released

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) ...
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MicroScope Winter break 2020

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 ...
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Supporting MicroScope’s future developments.

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 ...
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MicroScope professional trainings 2021

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 ...
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Functionality enhancements for genome integration requests

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 ...
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Interactive MA-plot and Counts-plot to improve the exploration of RNA-Seq DEG

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 ...
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