title: Use of AAScatterPlot tool for monitoring the evolution of the hemagglutinin cleavage site in H9 avian influenza viruses.
abstract: BACKGROUND
  Viruses rapidly evolve due to their error-prone genome replication, and identifying which mutations are selected for during evolution is critical for virus surveillance efforts. Here we introduce a scatter plot tool (AAScatterPlot) that easily shows the selection and avoidance of certain protein mutations based on biochemical properties. We demonstrate its utility for monitoring the evolution of H9 avian influenza viruses from China between 2005 and 2015, particularly at the hemagglutinin (HA) proteolytic cleavage site (PCS) that can affect virus activation and pathogenicity.
  
  
  RESULTS
  Given genome sequences, the AAScatterPlot tool compacts into a single plot, information about the hydropathy index, Van der Waals volume, chemical property and occurrence frequency of amino acid residues. The tool also shows the range of residues that could arise from a single point mutation in the genome, which can then be compared against the observed residues to identify mutation constraints. Through this approach, we found that the 2nd position towards the N-terminus side of the HA PCS (P2 position) avoided hydrophobic residues, whereas the P3 position avoided hydrophilic residues.
  
  
  METHODS
  AAScatterPlot is available at https://github.com/WhittakerLab/AAScatterPlot.
  
  
  BACKGROUND
  gary.whittaker@cornell.edu.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: School of Chemical and Biomolecular Engineering.
authors.forename: Donald W
authors.initials: DW
authors.lastname: Lee
authors.affiliation: Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA.
authors.forename: Gary R
authors.initials: GR
authors.lastname: Whittaker
mesh_terms: D000818:Animals; D001717:Birds / Q000821:virology; D019143:Evolution, Molecular; D023281:Genomics / Q000379:methods*; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics*; D009980:Influenza A virus / Q000235:genetics / Q000378:metabolism*; D005585:Influenza in Birds / Q000235:genetics / Q000378:metabolism*; D012984:Software
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus