How single mutations affect viral escape from broad and narrow antibodies to H1 influenza hemagglutinin
This directory contains the analysis of the mutational antigenic profiling of the A/WSN/1933 (H1N1) influenza virus hemagglutinin against a collection of broad and narrow antibodies.
The study was performed by Mike Doud, Juhye Lee, and Jesse Bloom in Bloom lab.
The analysis is performed by the Jupyter notebook analysis_notebook.ipynb. This notebook describes the results, and is what you should read to understand the analysis. Most parts of the analysis were performed using dms_tools2.
All generated results are placed in the created directory ./results/.
All required input data are in the ./data/ subdirectory. Specifically, this directory includes the following:
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./data/WSN_HA_reference.fa contains the wildtype sequence of the A/WSN/1933 (H1N1) HA used in this experiment.
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./data/samples.csv is a CSV file that specifies each sample, the SRA run that contains its deep sequencing data, and some other descriptive information.
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.data/H1toH3_renumber.csv is a CSV file that maps the numbering from sequential (1, 2, ...) numbering of the WSN HA protein sequence to the commonly used H3 numbering scheme. The sequential number is in the original column, and the H3 numbering is in the new column.
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./data/Overall-WSNHA_merged_prefs_rescaled_H3numbering.csv gives the site-specific amino-acid preferences for the A/WSN/1933 HA after being re-scaled to optimally fit natural sequence, as taken from the supplementary material of Doud and Bloom (2016).