Reannotation of the genome sequence of Clostridium difficile strain 630

Autor: Marc Monot, Ivan Moszer, Bruno Dupuy, Caroline Boursaux-Eude, Marie Thibonnier, Claudine Médigue, Isabelle Martin-Verstraete, David Vallenet
Přispěvatelé: Pathogénèse des Bactéries Anaérobies / Pathogenesis of Bacterial Anaerobes (PBA (U-Pasteur_6)), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7), Intégration et Analyse Génomique (Plate-Forme 4) (PF4), Institut Pasteur [Paris], Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université Paris Diderot - Paris 7 (UPD7), Université Paris Diderot - Paris 7 (UPD7)-Institut Pasteur [Paris], Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7), Institut Pasteur [Paris] (IP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Jazyk: angličtina
Rok vydání: 2011
Předmět:
Microbiology (medical)
Relational database
Molecular Sequence Data
MESH: Carrier Proteins
Computational biology
Biology
Bioinformatics
MESH: Genome
Bacterial
Microbiology
Genome
03 medical and health sciences
Annotation
Bacterial Proteins
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Genomics [q-bio.GN]
Gene
MESH: Bacterial Proteins
MESH: Clostridium difficile
030304 developmental biology
Sequence (medicine)
Whole genome sequencing
0303 health sciences
MESH: Gene Expression Regulation
Bacterial
MESH: Molecular Sequence Data
Clostridioides difficile
030306 microbiology
Cell Membrane
Nucleic acid sequence
Computational Biology
Enzyme Commission number
[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Molecular biology
Gene Expression Regulation
Bacterial
General Medicine
Carrier Proteins
Genome
Bacterial
MESH: Cell Membrane
MESH: Computational Biology
Zdroj: Journal of Medical Microbiology
Journal of Medical Microbiology, Society for General Microbiology, 2011, 60 (8), pp.1193-9. ⟨10.1099/jmm.0.030452-0⟩
Journal of Medical Microbiology, 2011, 60 (8), pp.1193-9. ⟨10.1099/jmm.0.030452-0⟩
ISSN: 1473-5644
0022-2615
DOI: 10.1099/jmm.0.030452-0⟩
Popis: International audience; A regular update of genome annotations is a prerequisite step to help maintain the accuracy and relevance of the information they contain. Five years after the first publication of the complete genome sequence of Clostridium difficile strain 630, we manually reannotated each of the coding sequences (CDSs), using a high-level annotation platform. The functions of more than 500 genes annotated previously with putative functions were reannotated based on updated sequence similarities to proteins whose functions have been recently identified by experimental data from the literature. We also modified 222 CDS starts, detected 127 new CDSs and added the enzyme commission numbers, which were not supplied in the original annotation. In addition, an intensive project was undertaken to standardize the names of genes and gene products and thus harmonize as much as possible with the HAMAP project. The reannotation is stored in a relational database that will be available on the MicroScope web-based platform (https://www.genoscope.cns.fr/agc/microscope/mage/viewer.php?S_id=752&wwwpkgdb=a78e3466ad5db29aa8fe49e8812de8a7). The original submission stored in the (International Nucleotide Sequence Database Collaboration) INSDC nucleotide sequence databases was also updated.
Databáze: OpenAIRE
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