| Title: |
ViralORFeome: an integrated database to generate a versatile collection of viral ORFs. |
| Authors: |
Pellet, J.; Tafforeau, L.; Lucas-Hourani, M.; Navratil, V.; Meyniel, L.; Achaz, Guillaume; Guironnet-Paquet, A.; Aublin-Gex, A.; Caignard, G.; Cassonnet, P.; Chaboud, A.; Chantier, T.; Deloire, A.; Demeret, Caroline; Le Breton, M.; Neveu, G.; Jacotot, L.; Vaglio, P.; Delmotte, Sebastien; Gautier, Christian; Combet, C.; Deleage, G.; Favre, M.; Tangy, F.; Jacob, Y.; Andre, P.; Lotteau, V.; Rabourdin-Combe, C.; Vidalain, P. O. |
| Contributors: |
Immunité infection vaccination (I2V); Université Claude Bernard Lyon 1 (UCBL); Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM); Génomique Virale et Vaccination; Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS); Rétrovirus et Pathologie Comparée (RPC); Institut National de la Recherche Agronomique (INRA)-École Pratique des Hautes Études (EPHE); Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Université Claude Bernard Lyon 1 (UCBL); Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL); BioSciences Lyon-Gerland (BLG); École normale supérieure de Lyon (ENS de Lyon); Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL); Université de Lyon-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS); Modul-Bio; Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE); Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS); Génétique, Papillomavirus et Cancer Humain; Institut Pasteur Paris (IP); Reproduction et développement des plantes (RDP); Université de Lyon-Centre National de la Recherche Scientifique (CNRS); Baobab LBBE; Département PEGASE LBBE (PEGASE); Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL); Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE); Institut de biologie et chimie des protéines Lyon (IBCP); Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS); The Institut National de la Santé et de la Recherche Médicale; the Institut National de la Recherche Agronomique; the Association de la Recherche contre le Cancer (3731XA0531F and 4867); the Ligue Nationale Contre le Cancer (RS07/75-75); the Agence Nationale de la Recherche (EPI-HPV-3D); the French Ministry of Industry; the Institut Pasteur; the Centre National de la Recherche Scientifique (Maladies Infectieuses Emergentes to P.O.V., G.C. and F.T.). Funding for open access charge: Institut Pasteur.; We thank all members of PF1-Pasteur Genopole sequencing core facility, in particular C. Bouchier and C. Gouyette. We thank Drs Marie-Louise Michel, Charles M. Rice, Kaoru Takeuchi, T. Fabian Wild and Ali Amara for providing RNA or DNA templates used to build viral ORF clones. We also thank Eric Coissac for providing SQL codes; ANR-07-MIME-0009,EPI-HPV-3D,Vers la compréhension fonctionelle et structurale de l'interactome cellulaire des protéines précoces des Papilloma Virus Humains.(2007) |
| Source: |
ISSN: 0305-1048. |
| Publisher Information: |
CCSD; Oxford University Press |
| Publication Year: |
2010 |
| Collection: |
HAL Lyon 1 (University Claude Bernard Lyon 1) |
| Subject Terms: |
User-Computer Interface; Software; Tertiary; Open Reading Frames; Information Storage and Retrieval; Genome; Genes; Genetic; Databases; Computational Biology; Cloning; Molecular; Nucleic Acid; Protein; Viral; Genetic Techniques; Internet; Protein Structure; MESH: Cloning; MESH: Computational Biology; MESH: Databases; MESH: Genes; MESH: Genetic Techniques; MESH: Genome; MESH: Information Storage and Retrieval; MESH: Internet; MESH: Open Reading Frames; MESH: Protein Structure; MESH: Software; MESH: User-Computer Interface |
| Description: |
International audience ; Large collections of protein-encoding open reading frames (ORFs) established in a versatile recombination-based cloning system have been instrumental to study protein functions in high-throughput assays. Such 'ORFeome' resources have been developed for several organisms but in virology, plasmid collections covering a significant fraction of the virosphere are still needed. In this perspective, we present ViralORFeome 1.0 (http://www.viralorfeome.com), an open-access database and management system that provides an integrated set of bioinformatic tools to clone viral ORFs in the Gateway(R) system. ViralORFeome provides a convenient interface to navigate through virus genome sequences, to design ORF-specific cloning primers, to validate the sequence of generated constructs and to browse established collections of virus ORFs. Most importantly, ViralORFeome has been designed to manage all possible variants or mutants of a given ORF so that the cloning procedure can be applied to any emerging virus strain. A subset of plasmid constructs generated with ViralORFeome platform has been tested with success for heterologous protein expression in different expression systems at proteome scale. ViralORFeome should provide our community with a framework to establish a large collection of virus ORF clones, an instrumental resource to determine functions, activities and binding partners of viral proteins. |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| Relation: |
info:eu-repo/semantics/altIdentifier/pmid/20007148; PRODINRA: 248430; PUBMED: 20007148; PUBMEDCENTRAL: PMC2808970; WOS: 000276399100058 |
| DOI: |
10.1093/nar/gkp1000 |
| Availability: |
https://pasteur.hal.science/pasteur-00455342; https://pasteur.hal.science/pasteur-00455342v1/document; https://pasteur.hal.science/pasteur-00455342v1/file/D371.pdf; https://doi.org/10.1093/nar/gkp1000 |
| Rights: |
https://creativecommons.org/licenses/by-nc/4.0/ ; info:eu-repo/semantics/OpenAccess |
| Accession Number: |
edsbas.89F92D5F |
| Database: |
BASE |