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ViralORFeome: an integrated database to generate a versatile collection of viral ORFs.

J. Pellet 1 L. Tafforeau 1 M. Lucas-Hourani 2 V. Navratil 3, 4 L. Meyniel 1 G. Achaz 5 A. Guironnet-Paquet 1, 6 A. Aublin-Gex 1 G. Caignard 2 P. Cassonnet 7 A. Chaboud 4, 8 T. Chantier 1 A. Deloire 1 Caroline Demeret 7 M. Le Breton 1 G. Neveu 7 L. Jacotot 5 P. Vaglio 5 Sebastien Delmotte 4, 6 Christian Gautier 4, 9 C. Combet 4, 10 G. Deleage 4, 10 M. Favre 7 F. Tangy 2 Y. Jacob 7 P. Andre 1, 4 V. Lotteau 1 C. Rabourdin-Combe 1, * P. O. Vidalain 2, *
* Corresponding author
1 I2V - Immunité infection vaccination
2 Génomique Virale et Vaccination
3 RPC - Rétrovirus et Pathologie Comparée
4 BLG - BioSciences Lyon-Gerland
5 Modul-Bio
6 LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
7 Génétique, Papillomavirus et Cancer Humain
8 RDP - Reproduction et développement des plantes
9 Baobab
PEGASE - Département PEGASE [LBBE]
10 IBCP - Institut de biologie et chimie des protéines [Lyon]
Abstract : 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.
Keywords : Cloning Computational Biology Databases Genetic Genes Genome Information Storage and Retrieval Open Reading Frames Tertiary Software User-Computer Interface
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Submitted on : Thursday, February 11, 2010 - 3:17:40 PM
Last modification on : Tuesday, July 20, 2021 - 5:20:05 PM
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J. Pellet, L. Tafforeau, M. Lucas-Hourani, V. Navratil, L. Meyniel, et al.. ViralORFeome: an integrated database to generate a versatile collection of viral ORFs.. Nucleic Acids Research, Oxford University Press, 2010, 38 (Issue suppl1: Database issue), pp.D371-8. ⟨10.1093/nar/gkp1000⟩. ⟨pasteur-00455342⟩

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