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.
Highlights
The use of high-throughput ‘-omics’ approaches produces a vast amount of information that needs to be efficiently integrated and analyzed to understand the biological meanings encoded in living organisms
We report a number of significant new developments in MicroScope over the last three years, including (i) improvements of the user interface of the genome browser and the gene editor and the design of new genome selectors (ii) the integration of new tools for functional annotation of genes and the characterization of genomic regions and (iii) comparative genomic functionalities based on pangenome graphs
Since 2017, several new tools for the functional annotation of genes and genomic regions have been integrated in MicroScope
Summary
The use of high-throughput ‘-omics’ approaches produces a vast amount of information that needs to be efficiently integrated and analyzed to understand the biological meanings encoded in living organisms. All genome submissions are processed through several analysis workflows for the syntactic and functional annotation (a detailed list of software and databases integrated in the MicroScope workflows is given in [8]). MicroScope supports collaborative expert annotation processes through the use of specific curation tools and graphical interfaces; it helps to develop hypotheses about specific genomes or sets of genes to be experimentally tested (examples are given in [6]).
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