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Nucleic Acids Research Advance Access published online on June 1, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm354
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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.

Web Server Issue

FLAN: a web server for influenza virus genome annotation

Yiming Bao, Pavel Bolotov, Dmitry Dernovoy, Boris Kiryutin and Tatiana Tatusova*

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

*To whom correspondence should be addressed. Tel: 301 435 5756; Email: tatiana{at}ncbi.nlm.nih.gov

Received February 1, 2007. Revised April 13, 2007. Accepted April 23, 2007.

FLAN (short for FLu ANnotation), the NCBI web server for genome annotation of influenza virus (http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/annotation.cgi) is a tool for user-provided influenza A virus or influenza B virus sequences. It can validate and predict protein sequences encoded by an input flu sequence. The input sequence is BLASTed against a database containing influenza sequences to determine the virus type (A or B), segment (1 through 8) and subtype for the hemagglutinin and neuraminidase segments of influenza A virus. For each segment/subtype of the viruses, a set of sample protein sequences is maintained. The input sequence is then aligned against the corresponding protein set with a ‘Protein to nucleotide alignment tool’ (ProSplign). The translated product from the best alignment to the sample protein sequence is used as the predicted protein encoded by the input sequence. The output can be a feature table that can be used for sequence submission to GenBank (by Sequin or tbl2asn), a GenBank flat file, or the predicted protein sequences in FASTA format. A message showing the length of the input sequence, the predicted virus type, segment and subtype for the hemagglutinin and neuraminidase segments of Influenza A virus will also be displayed.


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The Influenza Virus Resource at the National Center for Biotechnology Information
J. Virol., January 15, 2008; 82(2): 596 - 601.
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