MicroScope platform: v3.8 released

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 any bugs you may meet.

 

PS: Don’t forget to register for MicroScope Open Days

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MicroScope Winter break 2017

MicroScope services (integration of new genomic data) will be closed during Christmas and New Year holidays.
User support will also be very limited.

For maintenance reasons, MicroScope will be unavailable the 2nd of January 2018.

All Services will come back the 3th of January 2018.

The LABGeM team wishes you a happy holiday season.

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MicroScope Open Days – May 2018

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 context and improves community-based curation efforts. With more than 3500 user accounts and more than 750 citations, the platform has reached a high impact.
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Research Highlights: Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic 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 polysaccharides which are a major component of the cell walls of red macroalgae. Using a combination of biochemical, crystallographic, transcriptomic, genetic and bioinformatics techniques, this complex system has been characterized on an unprecedented scale within the field of marine biology. This is a major advancement towards understanding the molecular mechanisms governing the carbon cycle in coastal ecosystems. It is also a breakthrough for blue biotechnology and in particular the valorization of algal biomass.

Continue reading

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MicroScope professionnal trainings 2018

We are pleased to inform you about upcoming sessions of MicroScope professional training courses in 2018. Two complementary trainings are proposed:

Continue reading

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MicroScope: New tools IntegronFinder and MacSyFinder

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 spread of antibiotic resistance genes. More generally, integrons are gene-capturing platform, whose broader evolutionary role remains poorly understood. The detection methods use HMM profiles for the detection of the essential protein, the site-specific integron integrase and Covariance Models for the detection of attC sites.

You can access to the list of predicted integrons in a selected organism through the Integrons section of the Comparative genomics menu.

Macromolecular System Finder (MacSyFinder) v1.0.2 provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway) including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include functional analogs, and the multiple uses of a same component by different systems.

MacSyFinder can detect :

  • CRISPR-Cas systems: Clustered regularly interspaced short palindromic repeats (CRISPR) arrays and their associated Cas (CRISPR-associated) proteins form the CRISPR-Cas system. CRISPR-Cas are sophisticated adaptive immune systems that rely on small RNAs for sequence-specific targeting of foreign nucleic acids such as viruses and plasmids.
  • a broad range of secretion systems: T1SS, T2SS,T3SS,T4SS, T5SS, T6SS, T9SS, Flg, T4P, Tad (Abby SS et al., Sci. Rep. 2016)

You can access to the list of predicted systems in a selected organism through the Macromolecular Systems section of the Comparative genomics menu.

References:

Cury J. et al. 2016. Identification and analysis of integrons and cassette arrays in bacterial genomes. Nucleic Acids Research ; [PMID 27130947]

Abby SS, et al. 2014. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems, PLoS ONE 2014;9(10):e110726 ; [PMID 25330359]

 

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MicroScope platform: v3.7 released

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 at the same time. You can have more explication about the new export page here.
A small graphical update has also been made over all the platform.

Please report us any bugs you may meet.

 

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MicroScope maintenance

For maintenance reasons (database update), MicroScope will be shutdown on wednesday 15th november 2017 10:00 french time (8:00 UTC). We expect to be offline for 3H. We apologize for any inconveniences.

 

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Training: MicroScope – advanced course – december 2017

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 a few years ago. We will present new key features of the MicroScope platform as well as tools dedicated to RNA-seq analyses, and we will particularly focus on new features dedicated to the exploration of bacterial metabolism.

The training is organized at EVRY University. There are a few places left.

Registrations are open until november 7th:

  • Monday 4th December 2017 – Tuesday 5th December 2017
  • Price: 600 € (Includes all training materials and lunch for 2 days)

To register and get more details please visit our website:
https://www.genoscope.cns.fr/agc/microscope/training

 

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MicroScope maintenance

For maintenance reasons, the Genoscope’s servers will be shutdown from Friday 22th September 2017 16:30 (14:30 UTC) to Saturday 23th September 2017.

The MicroScope platform will be unavailable during this scheduled maintenance and will normally be back on Saturday evening.

We apologize for any inconveniences.

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