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: v3.16.3 released

The version 3.16.3 of the platform is now deployed: eggNOG results in MicroScope have been updated. We are now using the version 5 of eggNOG (http://eggnog5.embl.de) which includes a complete update of the genomes and functional databases. In addition to the functional annotations for each ortholog group (OG), COG categories ...

Retirement of MICHECK and AMIGene

Dear users, We have decided to retire our old web tools MICHECK and AMIGene. Those tools have not been maintained for several years and are no longer useful as they (and many others) are integrated in MicroScope. We will proceed during next week (2024-W02). The LABGeM Team ...

Register to MicroScope platform 20 years anniversary!

Over the past two decades, MicroScope has been a leading platform empowering microbiologists with powerful tools and resources to delve deep into the fascinating world of microbial genomics. To celebrate this milestone, we invite you to join us at the Genopole of Evry on September 26th 2023. During this day ...

Prediction of prophages and defense systems in MicroScope

Bacteriophages (phages) are the most abundant viruses on the planet. The majority of free-living prokaryotic species are thought to be infected by phages, as evidenced by the widespread presence of prophages in prokaryotic genomes. A prophage is a bacteriophage genome that is integrated into the genome of a prokaryote. Given ...

Integration of SulfAtlas in MicroScope

Sulfation is a crucial modification found in nearly all prokaryotic and eukaryotic organisms which drastically changes the physicochemical and biological properties of compounds. Sulfated biomolecules are highly diverse in structure and function. Sulfatases are key enzymes in sulfate metabolism, catalyzing the removal of sulfate groups according to hydrolytic or oxidative ...

antiSMASH 6.1.1 in MicroScope

The secondary metabolite gene cluster prediction tool antiSMASH has been updated to version 6.1.1 (Blin et al, 2021) on the MicroScope platform. This version increases the number of supported cluster types from 58 to 71, with a focus on the rules for ribosomally synthesized and post-translationally modified peptides (RiPPs). Outside ...

MicroScope platform: v3.16.1 released

The version 3.16.1 of the platform is now deployed. The main changes are: The new page Prophage & Defense System Prediction presents prediction of prophage (read more here). tMeV has been replaced by Morpheus on the Metabolic Profiles and RNA-Seq Differential Expression Analysis pages (read more here). The old RNA-Seq ...

MICROCYC server unavailable

Dear MicroScope user, We are in the process of updating MicroCyc results. During this update, results displayed on the associated web server (https://microcyc.genoscope.cns.fr/) won't be available. This should take roughly one week. We will inform you when the service will be operational again. We apologize for any inconvenience,The MicroScope Team ...

Error when requesting integration of GenBank’s genomes

A number of users have reported that they can't use the genome selector when requesting integration of GenBank's genomes (and thus can't submit the delivery of service). To the best of our knowledge, this happens only when using Chrome-based browsers (i.e. Google Chrome, MicroSoft Edge, and several others). It seems ...

New Genome cart functionality

A new functionality called "Genome Cart" has been integrated into the platform. It allows you to save one or more genome selection that are integrated in the selection component and can then be used in the different tools of the platform. The "Genome Cart" interface allows to create, edit, rename ...