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: v3.14.2 released

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 ...
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Fixed bugs in BLAST results

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 ...
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MicroScope platform: v3.14.1 released

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 ...
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MicroScope platform: v3.14.0 released

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 ...
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MicroScope platform: v3.13.5 released

The v3.13.5 of the platform is now deployed. As announced the new address of MicroScope is now https://mage.genoscope.cns.fr. The main changes are: More characters are allowed in the gene annotation page and invalid characters are better detected before validation.The tooltip of the synteny maps in taxon mode were wrong.The action ...
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Important changes to come in MicroScope

Dear MicroScope users, For technical reasons, we will soon change the address used to access MicroScope from your web browser: the current address will be replaced by https://mage.genoscope.cns.fr/microscope on Wednesday February 26th at 2:00PM CEST. At this date, the current address will redirect your browser to the new one so ...
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MicroScope professional trainings 2020.

We are pleased to inform you about MicroScope professional training courses in 2020. Two sessions of the «Annotation and analysis of prokaryotic genomes using the MicroScope platform» course are planned at the University of Evry: Monday 16th March 2020 – Friday 20th March 2020Monday 23rd November 2020 – Friday 27th ...
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New MicroScope paper in NAR-DB 2020 issue

A new MicroScope paper has just been published in the 2020 Database issue of Nucleic Acids Res. journal. This paper focuses on some major improvements since 2017: Improvements of the genome browser and of the sequence/organism selectorUpdate of the automatic annotation procedureNew tools for functional annotation of genes : eggNOG, ...
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Integration of antiSMASH 5 in MicroScope

The secondary metabolite gene cluster prediction tool antiSMASH has been updated to version 5 on the MicroScope platform. This new version includes updated and extended cluster identification profiles, and allows to detect 52 types of Biosynthetic Gene Clusters (BGCs) []. The program also offers extended and improved BGC detection and ...
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CRISPRCasFinder predictions in MicroScope

CRISPR (clustered regularly interspaced short palindromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic elements, such as phages or plasmids. CRISPRCasFinder [] allows the identification of both CRISPR arrays and Cas proteins (identified by MacSyFinder). The list of predicted systems in ...
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