Important usage notes:
The main application scenario for FluSurver is to highlight phenotypically or epidemiologically interesting candidate mutations for further research and should ideally be combined with experimental testing and verification of any predicted phenotypes. Importantly, any direct diagnostic use, assumed severity or recommendation on patient treatment should not be based solely on these computational predictions. Our curated reference sequences used for annotation transfer of equivalent mutations are mainly comprised of strains that recently infected humans. Therefore, the usage scenario that will give the most fruitful and reliable results are current surveillance sequences with very close relation to used vaccine strains, including some candidates for avian flu (including H5N1 and H7N9) and novel reassortant swine flu H3N2v. For most productive analysis of the recently widely spreading avian H5N8 please use our GISAID-FluSurver version (contact flusurver@gisaid.org for details!)

Please take a look at the Frequently Asked Questions and Tutorial if you are new to FluSurver. You could also look at this NA example analysis walkthrough and the GISAID access preview poster.

Paste your protein or nucleotide FASTA sequence(s) into the text area below. (Sample FASTA sequences: 2009 H1N1 NA and HA)
 
   
  OR upload your protein or nucleotide sequences in a FASTA file
 
   
  The server can automatically determine the type of input (either protein or nucleotide) and the closest reference sequence among current
vaccine strains to compare. Also mixtures of genes/proteins (e.g. HA and NA or all genes of the same patient) can be provided as input.
To compare with more remotely related sequences/strains, it is possible to select a specific reference strain by choosing below.
   
  Compare with:
   
  Additional settings:
  ignore low quality bases for nucleotide input (indicated by lower case, except for all lower case sequences)
  do not show result if alignment coverage is below 50% (useful for analyzing assembled contig files from NGS runs)
   
   (estimated time needed: ~2 seconds per sequence in automatic mode)