title: Reannotation of the genome sequence of Clostridium difficile strain 630.
abstract: 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.
authors.affiliation: Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, 28 Rue du Dr Roux, F-75724 Paris Cedex 15, France.
authors.forename: Marc
authors.initials: M
authors.lastname: Monot
authors.affiliation: Intégration et Analyse Génomiques, Institut Pasteur, 28 Rue du Dr Roux, F-75724 Paris Cedex 15, France.
authors.forename: Caroline
authors.initials: C
authors.lastname: Boursaux-Eude
authors.affiliation: Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, 28 Rue du Dr Roux, F-75724 Paris Cedex 15, France.
authors.forename: Marie
authors.initials: M
authors.lastname: Thibonnier
authors.affiliation: CNRS UMR 8030, Université d'Evry & CEA, IG, Genoscope - LABGeM, 2 Rue Gaston Crémieux, CP 5706, F-91057 Evry Cedex, France.
authors.forename: David
authors.initials: D
authors.lastname: Vallenet
authors.affiliation: Intégration et Analyse Génomiques, Institut Pasteur, 28 Rue du Dr Roux, F-75724 Paris Cedex 15, France.
authors.forename: Ivan
authors.initials: I
authors.lastname: Moszer
authors.affiliation: CNRS UMR 8030, Université d'Evry & CEA, IG, Genoscope - LABGeM, 2 Rue Gaston Crémieux, CP 5706, F-91057 Evry Cedex, France.
authors.forename: Claudine
authors.initials: C
authors.lastname: Medigue
authors.affiliation: Université Paris 7-Denis Diderot, 75205 Paris, France.|Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, 28 Rue du Dr Roux, F-75724 Paris Cedex 15, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Martin-Verstraete
authors.affiliation: Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, 28 Rue du Dr Roux, F-75724 Paris Cedex 15, France.
authors.forename: Bruno
authors.initials: B
authors.lastname: Dupuy
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D002462:Cell Membrane / Q000502:physiology; D016360:Clostridioides difficile / Q000145:classification* / Q000235:genetics*; D019295:Computational Biology; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D008969:Molecular Sequence Data
chemical_list: D001426:Bacterial Proteins; D002352:Carrier Proteins