ArticleNucleic acids research2020
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 211 papers.
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211 citing papers in PubMed.
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- Phylogenomic and metabolic insights into iron reduction metabolism in the genusMicrobial genomics · 2026Article
- Genome sequencing and comparative analysis of Nocardiopsis moroccensis sp. nov., a halotolerant Actinomycetota from Moroccan hypersaline ecosystem.BMC microbiology · 2026Article
- Identification of specific metabolic capacities associated with major extraintestinal pathogenicJournal of bacteriology · 2026Article
- Transcriptome, metabolome, and inflammatory and oxidative properties ofApplied and environmental microbiology · 2026Article
- Magnetoreception in a freshwater ciliate arises from endosymbiosis.Nature communications · 2026Article
- Genomic and functional insights into the thermophilic strain Geobacillus sp. Geo 8.1: a source of thermostable xylanase for sustainable bioprocesses.World journal of microbiology & biotechnology · 2026Article
- A novel North Sea ammonia-oxidizing archaeon Nitrosarchaeum marinum leverages a high abundance of transport systems to grow over a wide salinity range.FEMS microbiology ecology · 2026Article
- The interplay between the marine diazotrophApplied and environmental microbiology · 2026Article
- Elucidation of dimethyl sulfide assimilation in soil bacteria expands the enzymatic landscape of terrestrial sulfur cycling.The ISME journal · 2026Article
- Cultivation and molecular profiling reveal ammonia-oxidizing archaea as skin commensals.The ISME journal · 2026Article
- MagnetotacticISME communications · 2026Article
- Genomic signatures of radiation stress adaptations inFrontiers in microbiology · 2026Article
151 more citing papers are in PubMed but not listed here.
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Authors and funding
18 authors.
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Abstract
Large-scale genome sequencing and the increasingly massive use of high-throughput approaches produce a vast amount of new information that completely transforms our understanding of thousands of microbial species. However, despite the development of powerful bioinformatics approaches, full interpretation of the content of these genomes remains a difficult task. Launched in 2005, the MicroScope platform (https://www.genoscope.cns.fr/agc/microscope) has been under continuous development and provides analysis for prokaryotic genome projects together with metabolic network reconstruction and post-genomic experiments allowing users to improve the understanding of gene functions. Here we present new improvements of the MicroScope user interface for genome selection, navigation and expert gene annotation. Automatic functional annotation procedures of the platform have also been updated and we added several new tools for the functional annotation of genes and genomic regions. We finally focus on new tools and pipeline developed to perform comparative analyses on hundreds of genomes based on pangenome graphs. To date, MicroScope contains data for >11 800 microbial genomes, part of which are manually curated and maintained by microbiologists (>4500 personal accounts in September 2019). The platform enables collaborative work in a rich comparative genomic context and improves community-based curation efforts.
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