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

INSERM U851, Lyon, IFR128-BioSciences, Université Lyon 1, Université de Lyon, Lyon, France.
Nucleic Acids Research (Impact Factor: 9.11). 12/2009; 38(Database issue):D371-8. DOI: 10.1093/nar/gkp1000
Source: PubMed

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 (, 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.

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    • "ession vector encoding CHIKV structural proteins ( CHIKVsp ) was previously described ( Akahata et al . , 2010 ) and kindly provided by Dr . Gary Nabel of National Institute of Allergy Infectious Diseases . mCherry tagged plasmids encoding various CHIKV proteins ( nsP1 , nsP2 , nsP3 , nsP4 , E1 , E2 , E3 , Capsid , K6 ) were previously described ( Pellet et al . , 2010 ) and generously provided by Dr . Pierre - Olivier Vidalain of Unité de Gé nomique Virale et Vaccination , Institut Pasteur , France through Dr . Deborah Lenschow of Washington University School of Medicine , St . Louis , MO ."
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    • "To achieve recombinational cloning of PCR products, 5′ ends of forward primers were fused to attB1.1 recombination sequence 5′- GGGGACAACTTTGTACAAAAAAGTTGGCATG-3′, while reverse primers were fused to attB2.1 recombination sequence 5′-GGGGACAACTTTG- TACAAGAAAGTTGGTTA-3′. Primer pairs were designed using the ViralOrfeome interface (; Pellet et al., 2010). Recombination of PCR products into pDONR207 was performed following manufacturer's recommendation (BP cloning reaction, Invitrogen ). "
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