Laboratory of Bioinformatics Analyses for Genomics and Metabolism
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
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
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 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
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.
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
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
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
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
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
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
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
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.
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
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
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.
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.
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).
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 a program that allows the identification of both CRISPR arrays and Cas proteins has been integrated into MicroScope.
Discover the novel contextual menus added in the genome browser to ease the navigation and exploration of genomic objects or genomic regions.
Dear MicroScope users, We recently published an article describing the new functionalities in MicroScope to appear in the 2020 Nucleic Acids Research Database Issue. Please use this article when citing MicroScope. Thanks in advance,The LABGeM Team.
Mots-clefs : pangénome ; microbiologie environnementale ; évolution des génomes ; contexte génomique ; graphes La pangénomique vise à comprendre la variabilité génétique d’un groupe d’organismes, généralement d’une même espèce, en agrégeant l’information issue de l’ensemble des génomes disponibles plutôt que
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