SMILE

Stochastic Models for the Inference of Life Evolution

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

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

Nucleic Acids Research

2010

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.

Bibtex

@article{pellet_viralorfeome:_2010,
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.},
Title = {{ViralORFeome}: an integrated database to generate a
versatile collection of viral {ORFs}},
Journal = {Nucleic Acids Research},
Volume = {38},
Number = {Database issue},
Pages = {D371--378},
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.},
doi = {10.1093/nar/gkp1000},
issn = {1362-4962},
language = {eng},
month = jan,
pmcid = {PMC2808970},
pmid = {20007148},
shorttitle = {{ViralORFeome}},
year = 2010
}

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