AAScatterPlot

AAScatterPlot visualizes biochemical variation in aligned nucleotide and amino acid sequences to analyze selective pressures and constraints on protein mutations during viral evolution.

Key Features:

• Sequence analysis: Operates on aligned nucleotide and amino acid sequences to assess residue variation at specific protein sites.
• Biochemical property visualization: Generates scatter plots displaying hydropathy index, Van der Waals volume, chemical properties, and occurrence frequency of amino acid residues.
• Mutation possibility mapping: Highlights the range of amino acids that can arise from single nucleotide changes in the genome to compare observed versus theoretical substitutions.
• Selection and avoidance detection: Reveals patterns of selection or avoidance for specific residue types at critical sites by mapping biochemical properties against mutation frequency.

Scientific Applications:

• Influenza surveillance: Applied to monitor H9 avian influenza virus evolution in China (2005–2015), focusing on hemagglutinin (HA) proteolytic cleavage site (PCS).
• Site-specific selection analysis: Used to identify selective constraints at PCS positions, including avoidance of hydrophobic residues at P2 and avoidance of hydrophilic residues at P3.

Methodology:

Integrates aligned genomic (nucleotide and amino acid) sequence data with biochemical property information, computes occurrence frequencies and biochemical metrics (hydropathy, Van der Waals volume, chemical properties), and generates scatter plots that map mutation frequency and the range of amino acids possible from single-nucleotide changes.