Comparing amino-acid preferences across influenza HA subtypes

Analysis by Timothy Yu (2025)

See https://github.com/jbloomlab/ha-preference-shifts for full code.

Documentation of results rendered as of Sun Mar 8 21:33:25 2026

Analysis

Interactive plots

• Interactive lineplots of divergence in amino-acid preferences between pairs of HAs

Analysis notebooks

• Calculating pairwise sequence identities between HAs
• Structural alignment of H3, H5, and H7
• Calculating Jensen-Shannon divergence in amino-acid preferences between pairs of HAs
• Comparing mutation effects across different cell types
• Analysis of factors associated with divergence in amino-acid preferences
• Analysis of local neighborhood change versus divergence

Data files

• Structural alignment
• Mutation effects
• Average mutation effects at each site