Laboratory of Bioinformatics Analyses for Genomics and Metabolism
The MicroScope team was delighted to present a poster at JOBIM 2026, giving a comprehensive overview of the MicroScope platform and highlighting its latest developments. JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques), held this year in Strasbourg, France, is
Software updates and associated calculations for all genomes have been implemented in this version, including: — DefenseFinder 2.0.0. For more details, see our post : Antidefense system prediction using DefenseFinder The updated results are available on the “Prophages and Defense
The defense system prediction tool has been updated to DefenseFinder 2.0.0 on the MicroScope platform. In this context, the results of AntiDefenseFinder have been integrated. DefenseFinder is a bioinformatic tool for the systematic detection of anti-phage defense systems in prokaryotic
This version includes : For any questions or feedback, feel free to contact us.
Software updates and associated calculations for all genomes have been implemented in this version, including: — AMRFinderPlus 5.2.7 replacing CARD results. For more details, see our post : AMRFinderPlus replaces CARD for Antibiotic Resistance Prediction The updated results are available
The MicroScope platform now integrates antimicrobial resistance prediction results generated with AMRFinderPlus 4.2.7, replacing those previously obtained using CARD/RGI, thereby providing up-to-date data under an open license. AMRFinderPlus uses an AMR protein database, HMMs, a hierarchy of AMR protein families,
Software updates and associated calculations for all genomes have been implemented in this version, including: — dbCAN3 & run_dbcan 5.1.2. For more details, see our post : Enhanced CAZyme Annotation in MicroScope — Interproscan/5.75.106.0 We have also updated all calculations
The carbohydrate-active enzyme (CAZyme) prediction tool has been updated for dbCAN3 & run_dbcan 5.2.1 on the MicroScope platform. The tool continues to use DIAMOND (for sequence comparison against the CAZy database) and HMM (for comparison against CAZy families HMM profiles)
Version 3.18.0 of the platform is now available. This release upgrades the MicroScope codebase to ensure compatibility with a newer web server environment offering enhanced capabilities. Please report us any bugs you may meet.
Version 3.17.5 of the platform is now available. This version includes an update of the ‘genome overview’ page which features:– the updated calculations for GTDBtk according to release R220.– the updated calculations for CheckM according to version 1.2.3, and CheckM2/1.1.0 calculations
Version 3.17.3 of the platform is now available. It covers : We also corrected a few bugs Please report us any bugs you may meet.
Dear MicroScope Platform Users, We would like to inform you of a problem that has arisen with the Phigaro tool calculations on genomes. We have since resolved the issue and completed the necessary recalculations. You will now find the updated
The version 3.17.2 of the platform is now deployed: We also corrected a few bugs Please report us any bugs you may meet.
Dear MicroScope users, MicroScope will be off-line from Friday May 24th 5pm CEST to Monday May 27th around 8am CEST. This interruption is necessary to maintain the air conditioning system of our IT infrastructure. Services opened the week before might
The version 3.17.1 of the platform is now deployed: We also corrected a few bugs Please report us any bugs you may meet.
Dear MicroScope users, Due to a maintenance operation, Microscope will be unavailable for approximately 2 hours on Wednesday 17 April from 6am UTC . We apologise for any inconvenience caused. The LABGeM Team
The version 3.17.0 of the platform is now deployed: This version doesn’t bring any new features, but corresponds to a migration to a new web server. With this and some under the hood changes, MicroScope should be faster. We also
The version 3.16.4 of the platform is now deployed: We also changed a few things under the hood and corrected some bugs. Please report us any bugs you may meet.
The version 3.16.3 of the platform is now deployed: We also changed a few things under the hood and corrected some bugs. Please report us any bugs you may meet.
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
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
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
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 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
The version 3.16.1 of the platform is now deployed. The main changes are: Please report us any bugs you may meet.
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
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
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
To improve usability of the Genome Browser, the navigation bar has been redesigned: it is now placed above the genome map and has a reduced number of buttons. We also worked on the circular visualization of genomes in the platform.
Dear MicroScope users, MicroScope and LABGeM’s website will be unavailable starting Friday September 2th around 5pm CEST. Everything should be back to normal for Monday September 5th 9am CEST. This is needed for an maintenance operation on the electrical network
The version 3.16.0 of the platform is now deployed: The COG dataset ha been removed: this was needed because the version used in MicroScope was quite old (dating back to 2009). Users are encouraged to use the EggNOG classification tool.
Dear MicroScope users, You may have noticed that MicroScope was unavailable for several hours between yesterday and this morning (CEST). This is due to an unexpected problem on our SQL server. We are working on this problem and hope that
Dear MicroScope users, Microscope will be unavailable for a few minutes this evening, Monday July 18th around 5pm CEST . MicroScope will be off-line Friday July 22th 12pm CEST for about one hour. This is needed for adatabase maintenance operation.
We are pleased to inform you that there are places available for the next session of the course «Annotation and analysis of prokaryotic genomes using the MicroScope platform» which will take place from November 21 to 25, 2022. This course
We have decided to remove assemblies which have been deleted from the GenBank database (see the list here). If you need these genomes for your analyses, you can request the integration of their current assembly version from this page.
The version 3.15.4 of the platform is now deployed. The main novelty of this version is the introduction of Genome Carts. They are integrated in the Sequence/Organism selector so they can be selected quickly. This feature replaces the list of
Dear MicroScope users, MicroScope and LABGeM’s website will be unavailable starting Friday March 25th around 5pm CEST. Everything should be back to normal for Monday March 28th 9am CEST. This is needed for an maintenance operation on the electrical network
Dear MicroScope users, As you may have noticed, MicroScope was unavailable or extremely slow between Thursday March 17th around 5pm CEST and Friday March 18th 10am CEST. This is due to an unexpected failure in our IT infrastructure. No data
Dear MicroScope users, You may have noticed an unusual number of problems in some tools recently (generally ending with a big red error message). This is due to an update in our SQL server that turned on a more strict
The version v3.15.3 of the platform is now deployed: As mentioned in the last newsletter, you will be asked to update your personal information when upon login. Moreover you will be asked to update those information every year (see the
Dear MicroScope users, MicroScope will be off-line from Friday December 17th 12pm CEST to Monday December 20th around 2pm CEST. This long shut-down is needed to update several components of our IT infrastructure. Services opened the week before might take
In the spring of 2020, we conducted a satisfaction survey with over 1700 users of the MicroScope platform. With this survey we wanted to know more about the profile of our user community and their use of the platform for
In order to improve the selection of genomes, MicroScope 3.15.2 introduced the possibility to select genomes based on a subset of species-level metadata published in Joshua S. Madin et al., A synthesis of bacterial and archaeal phenotypic trait data. Sci
In order to improve the processing time of the genome analysis, we chose to replace NCBI blast with Diamond version 2 to perform protein sequence alignments (i.e. synteny computations and alignments against UniProt). Internal tests showed that the results obtained
We are pleased to inform you about MicroScope professional training courses in 2022. Two sessions of the «Annotation and analysis of prokaryotic genomes using the MicroScope platform» course are planned at the University of Evry: Monday 14th March 2022 – Friday 18th March
Dear MicroScope users, Due to a maintenance operation on several servers at Genoscope, MicroScope will be offline from Friday November 19th afternoon (5 pm CEST time) to Sunday November 21st (the precise time is not known yet). We apologize for
Dear MicroScope Users, We recently discovered that some gene fissions (shown on the Gene Fusion/Fission page) were not detected correctly: in some cases, when the gene is split in several parts, only one correspondence is displayed. Note that gene fusions
Dear MicroScope users, Due to a maintenance operation MicroScope will be offline for few hours on Thursday August 17th from 02:00PM CEST. We apologize for any inconvenience,The LABGeM team
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
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
We are happy to announce the publication of PANORAMA, a new computational tool developed by our team, in PLOS Computational Biology. It has been developed during the PhD thesis of Jérôme Arnoux. Why PANORAMA? Over the past decade, the explosion
The MicroScope team was delighted to present a poster at JOBIM 2026, giving a comprehensive overview of the MicroScope platform and highlighting its latest developments. JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques), held this year in Strasbourg, France, is