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Nucleic Acids Research Advance Access published online on May 30, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm365
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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FluGenome: a web tool for genotyping influenza A virus

Guoqing Lu1,2, Thaine Rowley1,2, Rebecca Garten3 and Ruben O. Donis3,*

1Department of Biology and 2Department of Computer Science, University of Nebraska at Omaha, Omaha, NE and 3Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA

*To whom correspondence should be addressed. Tel: 404 639 4968; Fax: 404 639 2350; Email: rdonis{at}cdc.gov

Received January 31, 2007. Revised April 3, 2007. Accepted April 25, 2007.

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.

The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors.


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