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

J. Pellet; L. Tafforeau; M. Lucas-Hourani; V. Navratil; L. Meyniel; G. Achaz; A. Guironnet-Paquet; A. Aublin-Gex; G. Caignard; P. Cassonnet; A. Chaboud; T. Chantier; A. Deloire; C. Demeret; M. Le Breton; G. Neveu; L. Jacotot; P. Vaglio; S. Delmotte; C. Gautier; C. Combet; G. Deleage; M. Favre; F. Tangy; Y. Jacob; P. Andre; V. Lotteau; C. Rabourdin-Combe; P. O. Vidalain

pasteur-00455342, version 1

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, C. Demeret ⁷, M. Le Breton ¹, G. Neveu ⁷, L. Jacotot ⁵, P. Vaglio ⁵, S. Delmotte ^4, 6, C. Gautier ^4, 6, C. Combet ^4, 9, G. Deleage ^4, 9, M. Favre ⁷, F. Tangy ², Y. Jacob ⁷, P. Andre ^1, 4, V. Lotteau ¹, C. Rabourdin-Combe ( Author to contact preferably ) ¹, P. O. Vidalain () ²

Nucleic Acids Research 38, Database issue (2010) D371-8

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.

1: Immunité infection vaccination
INSERM : U851 – IFR128 – Université Claude Bernard - Lyon I
2: Génomique Virale et Vaccination
Institut Pasteur de Paris – CNRS : URA3015
3: INRA : UMR754
Institut national de la recherche agronomique (INRA) : UMR754
4: BioSciences Lyon-Gerland (BLG)
CNRS : IFR128 – INSERM : IFR128 – Institut national de la recherche agronomique (INRA) – Hospices Civils de Lyon – Université Claude Bernard - Lyon I – École Normale Supérieure - Lyon
5: Modul-Bio
Modul-Bio
6: Laboratoire de Biométrie et Biologie Evolutive (LBBE)
Université Claude Bernard - Lyon I – CNRS : UMR5558 – INRIA
7: Génétique, Papillomavirus et Cancer Humain
Institut Pasteur de Paris
8: Reproduction et développement des plantes (RDP)
CNRS : UMR5667 – Institut national de la recherche agronomique (INRA) : UR0879 – Université Claude Bernard - Lyon I – École Normale Supérieure - Lyon
9: Institut de biologie et chimie des protéines [Lyon] (IBCP)
CNRS : UMR5086 – Université Claude Bernard - Lyon I

pasteur-00455342, version 1
http://hal-pasteur.archives-ouvertes.fr/pasteur-00455342
oai:hal-pasteur.archives-ouvertes.fr:pasteur-00455342
From: Mireille Gau <>
Submitted on: Thursday, 11 February 2010 15:17:40
Updated on: Thursday, 11 February 2010 15:19:34

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PubMed: 20007148

PubMed Central: 2808970

DOI: 10.1093/nar/gkp1000

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%% pasteur-00455342, version 1
%% http://hal-pasteur.archives-ouvertes.fr/pasteur-00455342
@article{pellet:pasteur-00455342,
    hal_id = {pasteur-00455342},
    url = {http://hal-pasteur.archives-ouvertes.fr/pasteur-00455342},
    title = {{ViralORFeome: an integrated database to generate a versatile collection of viral ORFs.}},
    author = {Pellet, J. and Tafforeau, L. and Lucas-Hourani, M. and Navratil, V. and Meyniel, L. and Achaz, G. and Guironnet-Paquet, A. and Aublin-Gex, A. and Caignard, G. and Cassonnet, P. and Chaboud, A. and Chantier, T. and Deloire, A. and Demeret, C. and Le Breton, M. and Neveu, G. and Jacotot, L. and Vaglio, P. and Delmotte, S. and Gautier, C. and Combet, C. and Deleage, G. and Favre, M. and Tangy, F. and Jacob, Y. and Andre, P. and Lotteau, V. and Rabourdin-Combe, C. and Vidalain, P. O.},
    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.}},
    language = {English},
    affiliation = {Immunit{\'e} infection vaccination , G{\'e}nomique Virale et Vaccination , INRA : UMR754 , BioSciences Lyon-Gerland - BLG , Modul-Bio , Laboratoire de Biom{\'e}trie et Biologie Evolutive - LBBE , G{\'e}n{\'e}tique, Papillomavirus et Cancer Humain , Reproduction et d{\'e}veloppement des plantes - RDP , Institut de biologie et chimie des prot{\'e}ines [Lyon] - IBCP},
    pages = {D371-8},
    journal = {Nucleic Acids Research},
    volume = {38},
    number = {Database issue },
    audience = {international },
    issn = {0305-1048 },
    doi = {10.1093/nar/gkp1000 },
    year = {2010},
    month = Jan,
    pdf = {http://hal-pasteur.archives-ouvertes.fr/pasteur-00455342/PDF/D371.pdf},
}

%F pasteur-00455342, version 1
%0 Journal Article
%U http://hal-pasteur.archives-ouvertes.fr/pasteur-00455342
%T ViralORFeome: an integrated database to generate a versatile collection of viral ORFs.
%A Pellet, J.
%A Tafforeau, L.
%A Lucas-Hourani, M.
%A Navratil, V.
%A Meyniel, L.
%A Achaz, G.
%A Guironnet-Paquet, A.
%A Aublin-Gex, A.
%A Caignard, G.
%A Cassonnet, P.
%A Chaboud, A.
%A Chantier, T.
%A Deloire, A.
%A Demeret, C.
%A Le Breton, M.
%A Neveu, G.
%A Jacotot, L.
%A Vaglio, P.
%A Delmotte, S.
%A Gautier, C.
%A Combet, C.
%A Deleage, G.
%A Favre, M.
%A Tangy, F.
%A Jacob, Y.
%A Andre, P.
%A Lotteau, V.
%A Rabourdin-Combe, C.
%A Vidalain, P. O.
%+ Immunité infection vaccination , Génomique Virale et Vaccination , INRA : UMR754 , BioSciences Lyon-Gerland - BLG , Modul-Bio , Laboratoire de Biométrie et Biologie Evolutive - LBBE , Génétique, Papillomavirus et Cancer Humain , Reproduction et développement des plantes - RDP , Institut de biologie et chimie des protéines [Lyon] - IBCP
%X 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.
%2 SDV:MP
%G English
%@ 0305-1048
%R 10.1093/nar/gkp1000
%J Nucleic Acids Research
%2 international
%8 2010-01-00
%V 38
%N Database issue
%P D371-8
%K Cloning, Molecular; Computational Biology; Databases, Genetic; Databases, Nucleic Acid; Databases, Protein; Genes, Viral; Genetic Techniques; Genome, Viral; Information Storage and Retrieval; Internet; Open Reading Frames; Protein Structure, Tertiary; Software; User-Computer Interface

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<orgName type="team">Immunité infection vaccination</orgName>
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<orgName type="institution">Institut Pasteur de Paris</orgName>
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<author><persName><forename>M.</forename><surname>Le Breton</surname></persName>
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<orgName type="team">Immunité infection vaccination</orgName>
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<orgName type="team">Génétique, Papillomavirus et Cancer Humain</orgName>
<country>FR</country>
<orgName type="institution">Institut Pasteur de Paris</orgName>
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<country>FR</country>
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<author><persName><forename>C.</forename><surname>Gautier</surname></persName>
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<orgName type="institution">CNRS : UMR5558</orgName>
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<author><persName><forename>C.</forename><surname>Combet</surname></persName>
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<orgName type="institution">Université Claude Bernard - Lyon I</orgName>
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<author><persName><forename>G.</forename><surname>Deleage</surname></persName>
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<orgName type="institution">Université Claude Bernard - Lyon I</orgName>
</affiliation>
</author>
<author><persName><forename>M.</forename><surname>Favre</surname></persName>
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<orgName type="institution">Institut Pasteur de Paris</orgName>
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<author><persName><forename>F.</forename><surname>Tangy</surname></persName>
<affiliation>
<orgName type="team">Génomique Virale et Vaccination</orgName>
<country>FR</country>
<orgName type="institution">Institut Pasteur de Paris</orgName>
<orgName type="institution">CNRS : URA3015</orgName>
</affiliation>
</author>
<author><persName><forename>Y.</forename><surname>Jacob</surname></persName>
<affiliation>
<orgName type="team">Génétique, Papillomavirus et Cancer Humain</orgName>
<country>FR</country>
<orgName type="institution">Institut Pasteur de Paris</orgName>
</affiliation>
</author>
<author><persName><forename>P.</forename><surname>Andre</surname></persName>
<affiliation>
<orgName type="team">Immunité infection vaccination</orgName>
<country>FR</country>
<orgName type="institution">INSERM : U851</orgName>
<orgName type="institution">IFR128</orgName>
<orgName type="institution">Université Claude Bernard - Lyon I</orgName>
</affiliation>
<affiliation>
<orgName type="laboratory">BLG</orgName>
<orgName type="team">BioSciences Lyon-Gerland</orgName>
<country>FR</country>
<orgName type="institution">CNRS : IFR128</orgName>
<orgName type="institution">INSERM : IFR128</orgName>
<orgName type="institution">Institut national de la recherche agronomique (INRA)</orgName>
<orgName type="institution">Hospices Civils de Lyon</orgName>
<orgName type="institution">Université Claude Bernard - Lyon I</orgName>
<orgName type="institution">École Normale Supérieure - Lyon</orgName>
</affiliation>
</author>
<author><persName><forename>V.</forename><surname>Lotteau</surname></persName>
<affiliation>
<orgName type="team">Immunité infection vaccination</orgName>
<country>FR</country>
<orgName type="institution">INSERM : U851</orgName>
<orgName type="institution">IFR128</orgName>
<orgName type="institution">Université Claude Bernard - Lyon I</orgName>
</affiliation>
</author>
<author><persName><forename>C.</forename><surname>Rabourdin-Combe</surname></persName>
<affiliation>
<orgName type="team">Immunité infection vaccination</orgName>
<country>FR</country>
<orgName type="institution">INSERM : U851</orgName>
<orgName type="institution">IFR128</orgName>
<orgName type="institution">Université Claude Bernard - Lyon I</orgName>
</affiliation>
</author>
<author><persName><forename>P. O.</forename><surname>Vidalain</surname></persName>
<affiliation>
<orgName type="team">Génomique Virale et Vaccination</orgName>
<country>FR</country>
<orgName type="institution">Institut Pasteur de Paris</orgName>
<orgName type="institution">CNRS : URA3015</orgName>
</affiliation>
</author>
<title type="main" level="a">ViralORFeome: an integrated database to generate a versatile collection of viral ORFs.</title></analytic><monogr><title level="j" type="main">Nucleic Acids Research</title><imprint><biblScope type="publicationDate">2010-01-00</biblScope><biblScope type="vol">38</biblScope><biblScope type="issue">Database issue</biblScope><biblScope type="pp">D371-8</biblScope></imprint></monogr><idno type="doi">10.1093/nar/gkp1000</idno><idno type="HALid">http://hal-pasteur.archives-ouvertes.fr/pasteur-00455342</idno><idno type="HALFile">http://hal-pasteur.archives-ouvertes.fr/pasteur-00455342/PDF/D371.pdf</idno></biblStruct>
</listBibl>
</listBibl>