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For seasonal influenza H1N1 an alignment of 2009 sequences prior to the swine flu outbreak (01/2009 to 03/2009) reveals that 85/89 have an N and 2/89 have K/H/T at amino acid 163, indicating that the N163K/H/T mutation is rare, but does exist at some low level in seasonal influenza (Influenza Virus Resources, [32]).
For validating the signatures obtained from analyzing the primary dataset, we further retrieved 15,785 human or avian influenza A viral protein sequences from NCBI's Influenza Virus Resources.
All available sequences of the hemagglutinin gene of HPAI (H5N1) viruses isolated from avian hosts were obtained from Influenza Virus Resources at the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/genomes/FLU/).nih.gov/genomes/FLU/
We subsequently validated the robustness of those signatures with human and avian protein sequences downloaded from Influenza Virus Resources at the National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html).nih.gov/genomes/FLU/FLU.html
For validating the obtained signatures from analyzing the mentioned 401-genome primary dataset, we have firstly retrieved 14,057 human or avian influenza A protein sequences from NCBI's Influenza Virus Resources (as of January 17 , 2006, including 5,468 avian and 8,589 human sequences (786 H1N1 sequences and 7,097 H3N2 sequences among the others).
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The Influenza Virus Resource is a database of influenza sequences and associated information [8].
For analysis of the evolution of influenza, genomes were taken from the Influenza Virus Resource at NCBI, (http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html).nih.gov/genomes/FLU/FLU.html
Comparative analysis of HA genes for all H5N1 viruses was carried out and compared with the available sequences using the NCBI influenza virus resource for both avian and human H5N1 viruses.
To compare the diversity within the segments of swine influenza A virus, we use strains deposited in the Influenza Virus Resource of the NCBI that have all eight segments completely sequenced.
In this paper, we employ the temporally and geographically diverse information deposited in the Influenza Virus Resource of the National Center for Biotechnology Information [27] to study the reassortment phenomena in swine influenza A viruses.
Published NA sequences of 1411 H5N1 influenza A viruses used for comparison were obtained from 1996 to 2007 from the Influenza Virus Resource (http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html).nih.gov/genomes/FLU/FLU.html
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