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The platform MicroScope was launched in 2002 by LABGeM (Genoscope) to provide the international microbiology community with bioinformatics tools for the analysis and exploration of prokaryote genomes. The platform's innovations were recently highlighted in a special edition of Nucleic Acids Research on databases. The journal's readers can discover MicroScope's recent developments for the functional annotation of genes, the characterization of genomic islands, and the analysis of pan-genomes.
The large-scale sequencing of genomes and the
increasing use of high throughput technologies have provided large amounts of
data, and in so doing, transformed the acquisition of knowledge on thousands of
Nonetheless and despite the development of powerful
bioinformatics approaches, the complete interpretation of this genomic content
remains difficult. The microbial genome annotation and analysis platform
MicroScope was launched in 2002 within Genoscope's Laboratory of Bioinformatics
Analyses for Genomics and Metabolism (LABGeM). It has been under continuous
development since. MicroScope provides an array of tools for research on
prokaryote genomes, metabolic pathways, post-genomics and more, with which its
users can contribute to knowledge on gene function.
In a special edition of Nucleic Acids Research on
databases, LABGeM presented the most recent developments at MicroScope.
User interface improvements for genome selection and
to the genome browser and gene annotation editor were highlighted, as were the
updates made for automated functional annotation and the addition of new tools
for gene function annotations and genomic region characterization. The platform
also proposes tools for comparative analyses on hundreds of genomes based on
Currently, MicroScope houses data on more than 12,300
microbial genomes, a portion of which is conserved manually by microbiologists
(more than 4,700 personal accounts as of January 2020). The platform enables
collaborative work in a rich genomic context and contributes to the scientific
community's efforts for the conservation and curation of data.
1 : The term pan-genome describes the entire set of genes in a species. It
comprises thus all the genes from all of the strains within a species.
Pan-genomes are of importance in an evolutionary context, particularly in
metagenomics, but they are also useful in the larger context of general
MicroScope : an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis I Nucleic Acids Research
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