Located at Genoscope (the French National Sequencing Center), the LABGeM bioinformatics team has developed MicroScope (Vallenet et al., 2006, 2009, 2013) which is a web-based platform for microbial comparative genome analysis and manual functional annotation.
Its relational database schema stores precalculated results of syntactic and functional annotation pipelines as well as Pathway Tools metabolic analysis specific to each genome. PkGDB is also linked to these metabolic pathway databases (MicroCyc). The MicroScope web interface (MaGe, for « Magnifying Genomes » ) has been specifically designed to assist curators in the evaluation of all available data needed for assigning the best possible annotation to a given gene product. These data are:
- sequence-based (e.g., InterPro domain predictions),
- context-based (i.e., synteny results and metabolic network predictions),
- experimental (e.g., growth experiments, if any),
Moreover, MicroScope offers many useful data-exploring functionalities, such as allowing users to perform (complex) queries, comparative genomic studies, and metabolic analyses. It also provides summary views of statistics and information for each genome as a whole. Finally, MicroScope can be used both as:
- a community resource, for comparative analysis and annotation of publicly available genomes
- a private resource, as access rights to private projects can be restricted to a limited group of annotators defined by the project leader.
- (re)Annotation and comparative analyses of finished or draft genome sequences.
- Annotation and comparative analyses of metagenomic sequences. Currently, we are able to integrate datasets below 20 Mb.
- RNA-Seq analysis
- Map a RNA-Seq dataset to a reference genome and perform differential expression analyses.
- Variant profiling
- SNP/indels detection among different evolved strains by comparison with a reference genome.
- Please check the « LABGeM's service offer » to get more information about setting up a new project.
- «MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis», Nucleic Acids Res., 2019 Oct. 24.
- «MicroScope -- an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data», Brief Bioinform, 2017 Sep. 12.
- «MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes», Nucleic Acids Res., 2016 Nov..
- «MicroScope -- an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data», Nucleic Acids Res., 2013 Jan..
- «MicroScope: a platform for microbial genome annotation and comparative genomics», Database (Oxford), 2009.
- «MaGe: a microbial genome annotation system supported by synteny results», Nucleic Acids Res., 2006 Jan. 10.