Laboratory of Bioinformatics Analyses for Genomics and Metabolism
Due to network maintenance at Genoscope, MicroScope may be unavailable on Tuesday October 15th between 12:00 pm and 2:00pm CEST for about 30mn. We apologize for any inconveniences.
The v3.13.3 of the platform is now deployed. Two important features were added in this version: The Macromolecular Systems page now displays CRISPR arrays found by CRISPRCasFinder. The Secondary Metabolites page has been updated to the brand new antiSMASH 5.0.
The v3.13.2 of the platform is now deployed. The main feature is the possibility to highlight a genomic region (as found for example by AntiSMASH or MacSyFinder) in the viewer. The contextual menu has 2 new options: you can explore
The v3.13.1 of the platform is now deployed. This release doesn’t introduce new features but fixes some bugs of v3.13.0 (or from older versions): the selector sometimes didn’t work in phyloprofile favourite organisms were not always properly saved the color
A new selector for sequences and organisms that extends the one previously introduced in the Genome Clustering page has been deployed in MicroScope since the end of June 2019. This selector was designed to let you choose efficiently several sequences by browsing the taxonomy or by filtering on strains with suggestions.
Delineating a set of essential genomic elements and proteins that make up a living organism helps to understand critical cellular processes that sustain life. Essential genes in a bacterium constitute a minimal genome, forming a set of functional modules, which play key roles in the emerging field of synthetic biology. A new ‘essential gene’ dataset coming from Database of Essential Genes (DEG) has been set up in MicroScope.
We are pleased to inform you about upcoming sessions of MicroScope professional training courses in 2019-2020.
The user interface dedicated to delivery of service in MicroScope has been improved. It is now possible to ask for the integration of public genome sequences. The list of available organisms from NCBI GenBank is up-to-date and give you access to > 202,000 entries.
The v3.13.0 of the platform is now deployed. There are 2 major features in this version: => First, there is a new selector for sequences and organisms that extends the one previously introduced in the Genome Clustering page. This selector
The v3.12.4 of the platform is now deployed: The tree in the Genome Clustering page can now be exported in Newick format (either with the full name or just with the taxid) Adobe Flash is no longer needed to export
Dear MicroScope users, We have recently made some changes in order to clarify MicroScope’s main menu: to integrate your data in MicroScope, go to “About” and then “Submit your data to MicroScope“ to submit your data to the ENA/EMBL public
The v3.12.3 of the platform is now deployed. What’s new in this version: There is a new dataset available in the Search by Keyword page and on the Gene Annotation page: the Essential gene results dataset contains genes that are
The v3.12.2 of the platform is now deployed: What’s new in this version: The Virulence Detection has been updated: it now includes blastN results to detect regions of virulence. We have updated the CGView applet: you can now maximize the
The v3.12.1 of the platform is now deployed. What’s new in this version: the main page of RNAseq experiments analysis has been improved the design of the Keyword Search has been improved: the “Explore More” feature is more intuitive and
The v3.12.0 of the platform is now deployed. The highlight of this new version is the integration of a new annotation method based on the UniRules. Read more about it here. As usual, we have fixed bugs and made little
A new functionality to search for potentially horizontally transferred genes (HGT) which are gathered in Region of Genomic Plasticity is available in MicroScope. The PanRGP tool is based on the PPanGGOLiN method. PPanGGOLiN (Partitioned PanGenome Graph Of Linked Neighbors) computes pangenomes taking
To meet the requirement of the GDPR, the new data protection EU law, we would like to inform you that we have updated the Terms of Use of the MicroScope platform. We now provide a Privacy Notice that describes why and how
We are pleased to inform you about an upcoming session of MicroScope professional training courses in March 2019: «Annotation and analysis of prokaryotic genomes using the MicroScope platform» 4.5 days training including 1 day fully dedicated to bacterial metabolism analyses, exploration
The v3.11.1 of the platform is now deployed. Here are some highlights of this new version: A new tool has been added: Pan-genome RGPs allows to explore regions of genomic plasticity based on a new definition of the pan-genome (read
The v3.10.3 of the platform is now deployed. Here are some highlights of this new version: There is some change on the resistome page as CARD/RGI has been updated to version 2.0.1 and 4.0.2 respectively. You can now extract EGNOGG
v3.10.0 of the platform is now deployed. Here are some highlights of this new version: There is a new tool called “Genome clustering” (under “Comparative Genomics”) which allows to group organisms according to their genomic similarity. It also features a
The registration to the MicroScope Open Days will be closed on May 2nd 2018. During 2 half days, 9 invited speakers will share their experience on using MicroScope for their research projects. Also live demos will be presented to highlight recent developments
The secondary metabolite gene cluster prediction tool antiSMASH has been updated to version 4 on the MicroScope platform. This new version includes updated and extended cluster identification profiles, especially for ribosomally synthesised peptide products (RiPPs) [1]. The ClusterFinder algorithm is also
eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations.
In January 2018, the Quality Management System of the LABGeM team has been renewed according the new NFX 50-900:2016 standard, which is specific to life science technology platforms and includes the the ISO 9001:2015 standard (Lloyd’s Register Quality Assurance France
The v3.9.2 of the platform is now deployed. It includes some enhancements: – The Blast page has been improved and is now faster. – It’s possible to set mutation at ‘alternative start’ in the gene annotation page. – When you
A PhD position is open at the LABGeM (Laboratory of Bioinformatics Analyses for Genomics and Metabolism). Our team is one of the bioinformatics labs of the Genoscope (CEA, French Genome Institute) located in Evry (35 kms south of Paris). Our areas of
The v3.9 of the platform is now deployed. It includes the following new features and enhancements: – EGGNOG version 4.5.1 is now available on the platform allowing new functional annotations and classification . – We have also improved Interpro result
The v3.8 of the platform is now deployed: antiSMASH version 4 is now available, it includes new features: – Better detection of secondary metabolite clusters – Alternative clusters coordinates We have also updated Interpro and KEGG related data. Please report us
Since its first publication in 2006, the MicroScope platform emulates the microbiologists community in France and worldwide. MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic genomes. The platform enables collaborative work in a rich comparative genomic
An international consortium coordinated by the Marine Glycobiology team (UMR8227 – CNRS/UPMC) has just published the discovery of the complete system for the utilization of carrageenans, sulfated polysaccharides which are a major component of the cell walls of red macroalgae.
We are pleased to inform you about upcoming sessions of MicroScope professional training courses in 2018. Two complementary trainings are proposed:
Two new detection tools are available in Microscope in the ‘Comparative Genomics’ menu IntegronFinder and MacSyfinder. IntegronFinder v1.5.2 is able to detect with high accuracy integron in DNA sequences. Integrons are major genetic element, notorious for their major implication in the
Discovery of the complete catabolic pathway for red algal carrageenans in marine bacteria An international consortium coordinated by the Marine Glycobiology team (UMR8227 – CNRS/UPMC) has just published the discovery of the complete system for the utilization of carrageenans, sulfated
The v3.7 of the platform is now deployed. The gene annotation page has been improved with a better visualization for additional data. The export page has been through a lot of change. You can now export genome of several organism
The next session of the « MicroScope platform – Advanced course » will be held next december. This 2 days training course is aimed at presenting the last developments of the MicroScope platform to users who have followed a MicroScope training
In order to fit the evolutions of technologies and usages and to constantly provide high quality tools, it has been decided to close the Variant Discovery Service Offer until further notice. The improvment of the service will focus on the
The gene annotation editor has been improved with a more accurate form and a better inconsistency check.
The Genome Browser has been updated to enhance visibility of genomic objects. In the viewer you can notice that the central part is now grey to separate the reverse strand from the direct one. In this central part are represented
The v3.5 of the platform is now deployed. The Genome Browser has been updated to enhance visibility of genomic objects. New functionalities have also been added to ease the navigation and exploration of genomic objects on the genome and in
The v3.4 of the platform is now deployed. InterPro results have been updated to version 5.22-61.0. Some other change have also been made: The query speed of TrEMBL/Swiss-Prot keyword search has been enhanced Antibiotic Resistance page has been renamed Resistome
We are pleased to inform you about upcoming sessions of MicroScope professional training courses in autumn 2017 and spring 2018. Two complementary trainings are proposed:
CEA-Genoscope, a dynamic non-profit scientific research organization dedicated to environmental genomics science, is seeking a talented and highly motivated bioinformatics software engineer: Research Engineer, IR CNRS permanent position in the LABGeM team UMR8030.
Virulence gene detection by BLASTp has been integrated on the MicroScope platform. The database is based on VFDB, VirulenceFinder and E. coli reference data. In order to ease the functional interpretation of the results, a virulence factor classification from VFDB
ASMC method (Active Sites Modeling and Clustering) is a novel unsupervised method to classify sequences using structural information of protein pockets. The method predicts functional amino-acids by proposing active site SDP residues (Specificity Determining Position) and active site CP residues
The v3.2 of the platform is now deployed. Some enhancements have been made to the “Blast and Pattern search” page: Blast search now use ncbi-blast+ v 2.2.28 Result can be filter with similarity constraints values (query coverage and identity) Pattern search
We are pleased to inform you about upcoming sessions of MicroScope professional training courses in 2017. Two complementary courses are proposed:
The v3.1 of the platform is now deployed. New functionalities are available on the “Export Data” page: Split data by contig/scaffold The format genbank, embl and gff have been updated Clicking on links now directly download the data (except for
A new MicroScope paper has just been published in the 2017 Database issue of Nucleic Acids Res. journal. This paper focuses on some major improvements since 2013: Web interface for the submission of genomic data Computation of pan-genomes Prediction of
The antibiotic resistance prediction of CARD has been integrated on the MicroScope platform. The Comprehensive Antibiotic Resistance Database CARD is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis
Contexte : Le Genoscope (CEA, Institut de Biologie François Jacob) est un centre de référence français en génomique environnementale qui réalise des analyses à grande échelle pour la compréhension des écosystèmes, notamment dans le contexte des grands changements environnementaux. Son
Analyse pangénomique des voies métaboliques chez les archées Description Lieu : Vous serez accueilli au sein du Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme (LABGeM, UMR8030, https://labgem.genoscope.cns.fr) du Genoscope (Institut de biologie François Jacob – CEA – Evry),