ArticleDatabase : the journal of biological databases and curation2009
MicroScope: a platform for microbial genome annotation and comparative genomics.
Article in Database : the journal of biological databases and curation, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 188 papers, 2 of them syntheses that pooled it.
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Who cites it
188 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Genomic evolution and adaptation of arthropod-associated Rickettsia.Scientific reports · 2022Pooled it
- Meta-analysis of theMicrobial genomics · 2022Pooled it
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- Quorum sensing rewires membrane vesicle protein cargo to promote antibiotic persistence inJournal of bacteriology · 2026Article
- Diversity of biofilm architectures within the genusApplied and environmental microbiology · 2026Article
- Genome-based analysis of Bacillus velezensis Bm3 isolated from a vulnerable dioxin-contaminated site in central Syria reveals mechanisms of dioxin degradation.Scientific reports · 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
- Complex compositional and metabolic response of river sediment microbiomes to multiple anthropogenic stressors.ISME communications · 2026Article
- STAGE: A compact and versatile TnpB-based genome editing toolkit forProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genome-Informed Real-Time PCR Assay for Detection of 'Microorganisms · 2025Article
- Diversity and functional features of the root-associated bacteriome are dependent on grapevine susceptibility to Plasmopara viticola.Environmental microbiome · 2025Article
- Growth of complete ammonia oxidizers on guanidine.Nature · 2024Article
- The multiplicity of thioredoxin systems meets the specific lifestyles of Clostridia.PLoS pathogens · 2024Article
- Transcriptome Analysis ofGenes · 2023Article
- Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta.The ISME journal · 2023Article
- Complete Genome Sequence ofMicrobiology resource announcements · 2023Article
- A Framework for the Systematic Selection of Biosensor Chassis for Environmental Synthetic Biology.ACS synthetic biology · 2022Review
- Mining Biosynthetic Gene Clusters inMicroorganisms · 2022Article
- Microaerobic enrichment of benzene-degrading bacteria and description of Ideonella benzenivorans sp. nov., capable of degrading benzene, toluene and ethylbenzene under microaerobic conditions.Antonie van Leeuwenhoek · 2022Article
- Integrating Genome-Resolved Metagenomics with Trait-Based Process Modeling to Determine Biokinetics of Distinct Nitrifying Communities within Activated Sludge.Environmental science & technology · 2022Article
128 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http://www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope's rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of microbial genome annotation, especially for genomes initially analyzed by automatic procedures alone.Database URLs: http://www.genoscope.cns.fr/agc/mage and http://www.genoscope.cns.fr/agc/microcyc.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.