FluGenome: A web tool for genotyping influenza A virus

Guoqing Lu; Thaine Rowley; Rebecca Garten; Ruben O. Donis

doi:10.1093/nar/gkm365

FluGenome: A web tool for genotyping influenza A virus

Guoqing Lu, Thaine Rowley, Rebecca Garten, Ruben O. Donis

Research output: Contribution to journal › Article › peer-review

71 Scopus citations

Abstract

Influenza A viruses are hosted by numerous avian and mammalian species, which have shaped their evolution into distinct lineages worldwide. The viral genome consists of eight RNA segments that are frequently exchanged between different viruses via a process known as genetic reassortment. A complete genotype nomenclature is essential to describe gene segment reassortment. Specialized bioinformatic tools to analyze reassortment are not available, which hampers progress in understanding its role in host range, virulence and transmissibility of influenza viruses. To meet this need, we have developed a nomenclature to name influenza A genotypes and implemented a web server, FluGenome (http://www.flugenome.org/), for the assignment of lineages and genotypes. FluGenome provides functions for the user to interrogate the database in different modalities and get detailed reports on lineages and genotypes. These features make FluGenome unique in its ability to automatically detect genotype differences attributable to reassortment events in influenza A virus evolution.

Original language	English (US)
Pages (from-to)	W275-W279
Journal	Nucleic acids research
Volume	35
Issue number	SUPPL.2
DOIs	https://doi.org/10.1093/nar/gkm365
State	Published - Jul 2007

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkm365

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title = "FluGenome: A web tool for genotyping influenza A virus",

abstract = "Influenza A viruses are hosted by numerous avian and mammalian species, which have shaped their evolution into distinct lineages worldwide. The viral genome consists of eight RNA segments that are frequently exchanged between different viruses via a process known as genetic reassortment. A complete genotype nomenclature is essential to describe gene segment reassortment. Specialized bioinformatic tools to analyze reassortment are not available, which hampers progress in understanding its role in host range, virulence and transmissibility of influenza viruses. To meet this need, we have developed a nomenclature to name influenza A genotypes and implemented a web server, FluGenome (http://www.flugenome.org/), for the assignment of lineages and genotypes. FluGenome provides functions for the user to interrogate the database in different modalities and get detailed reports on lineages and genotypes. These features make FluGenome unique in its ability to automatically detect genotype differences attributable to reassortment events in influenza A virus evolution.",

author = "Guoqing Lu and Thaine Rowley and Rebecca Garten and Donis, {Ruben O.}",

note = "Funding Information: The authors thank internal and outside users who tested FluGenome. We are grateful to Liying Jiang for her help with web programming at the early stage of this project. G.L. acknowledges the University of Nebraska at Omaha UCR grant for funding support. RG was supported in part by an Emerging Infectious Diseases (EID) Fellowship administered by the Association of Public Health Laboratories (APHL) and funded by the Centers for Disease Control and Prevention (CDC). Funding to pay the Open Access publication charges for this article was provided by CDC.",

year = "2007",

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doi = "10.1093/nar/gkm365",

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N1 - Funding Information: The authors thank internal and outside users who tested FluGenome. We are grateful to Liying Jiang for her help with web programming at the early stage of this project. G.L. acknowledges the University of Nebraska at Omaha UCR grant for funding support. RG was supported in part by an Emerging Infectious Diseases (EID) Fellowship administered by the Association of Public Health Laboratories (APHL) and funded by the Centers for Disease Control and Prevention (CDC). Funding to pay the Open Access publication charges for this article was provided by CDC.

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N2 - Influenza A viruses are hosted by numerous avian and mammalian species, which have shaped their evolution into distinct lineages worldwide. The viral genome consists of eight RNA segments that are frequently exchanged between different viruses via a process known as genetic reassortment. A complete genotype nomenclature is essential to describe gene segment reassortment. Specialized bioinformatic tools to analyze reassortment are not available, which hampers progress in understanding its role in host range, virulence and transmissibility of influenza viruses. To meet this need, we have developed a nomenclature to name influenza A genotypes and implemented a web server, FluGenome (http://www.flugenome.org/), for the assignment of lineages and genotypes. FluGenome provides functions for the user to interrogate the database in different modalities and get detailed reports on lineages and genotypes. These features make FluGenome unique in its ability to automatically detect genotype differences attributable to reassortment events in influenza A virus evolution.

AB - Influenza A viruses are hosted by numerous avian and mammalian species, which have shaped their evolution into distinct lineages worldwide. The viral genome consists of eight RNA segments that are frequently exchanged between different viruses via a process known as genetic reassortment. A complete genotype nomenclature is essential to describe gene segment reassortment. Specialized bioinformatic tools to analyze reassortment are not available, which hampers progress in understanding its role in host range, virulence and transmissibility of influenza viruses. To meet this need, we have developed a nomenclature to name influenza A genotypes and implemented a web server, FluGenome (http://www.flugenome.org/), for the assignment of lineages and genotypes. FluGenome provides functions for the user to interrogate the database in different modalities and get detailed reports on lineages and genotypes. These features make FluGenome unique in its ability to automatically detect genotype differences attributable to reassortment events in influenza A virus evolution.

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FluGenome: A web tool for genotyping influenza A virus

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