README.md

Sequence analysis of influenza hemagglutinin (HA) antibodies

This README describes the analysis in:
An explainable language model for antibody specificity prediction using curated influenza hemagglutinin antibodies

Contents

• Env setup
• Dataset
• CDR H3 analysis
• mBLM for specificity prediction

Env setup

if you set up env using conda, run conda installation as follow:

conda env create -f Ab_epitope/environment.yml

Dataset

• Flu antibody dataset in this paper: ./doc/HA_Abs_v18.xlsx
• SARS-CoV-2 antibody and HIV dataset is from our previous paper: A large-scale systematic survey reveals recurring molecular features of public antibody responses to SARS-CoV-2
• All antibody from NCBI./doc/all_paired_antibodies_from_GB_v6.xlsx: List of HA antibodies collected from GenBank
• OSA human paired memory B cell sequences: OAS

CDR H3 analysis

1. Extract CDR H3 sequences and references
   python3 script/parse_Ab_table.py

   • Input file:
     • ./doc/HA_Abs_v18.xlsx
   • Output files:
     • ./result/CDRH3.tsv
     • ./result/refs.txt

2. Clustering CDR H3 sequences
   python3 script/CDRH3_clustering_optimal.py

   • Input file:
     • ./result/CDRH3.tsv
   • Output file:
     • ./result/CDRH3_cluster.tsv

3. Analyzing CDR H3 clustering results
   python3 script/analyze_CDRH3_cluster.py

   • Input files:
     • ./doc/HA_Abs_v18.xlsx
     • ./result/CDRH3_cluster.tsv
   • Output files:
     • ./result/Ab_info_CDRH3_clustering.tsv
     • ./result/CDRH3_cluster_summary.tsv

4. Analyzing CDR H3 property
   python3 script/analyze_CDRH3_property.py

   • Input files:
     • ./doc/HA_Abs_v18.xlsx
     • ./doc/all_paired_antibodies_from_GB_v6.xlsx
     • ./result/HA_Abs_clonotype.xlsx
   • Ouput files:
     • ./result/CDRH3_property.tsv
     • ./result/Ab_for_model.tsv

5. Create sequence logos for different CDR H3 clusters
   python3 script/CDRH3_seqlogo.py

   • Input file:
     • ./result/Ab_info_CDRH3_clustering.tsv
   • Output file:
     • ./CDRH3_seqlogo/*.png

6. Plot CDR H3 property for HA head and stem antibodies
   Rscript script/plot_CDRH3_property.R

   • Input file:
     • ./result/CDRH3_property.tsv
   • Output files:
     • ./graph/CDRH3_length.png
     • ./graph/CDRH3_hydrophobicity.png
     • ./graph/tip_hydrophobicity.png

Germline usage analysis

1. Clonotype assignment
   python3 script/assign_clonotype.py

   • Input files:
     • ./doc/HA_Abs_v18.xlsx
     • ./result/CDRH3_cluster.tsv
   • Output file:
     • ./result/HA_Abs_clonotype.xlsx

2. Compute germline usag and extract public clonotype
   python3 script/extract_public_clonotype_VDJ.py

   • Input files:
     • ./doc/HA_Abs_v18.xlsx
     • ./doc/all_paired_antibodies_from_GB_v6.xlsx
     • ./result/HA_Abs_clonotype.xlsx
   • Output files:
     • ./result/IGHV_freq.tsv
     • ./result/IGHD_freq.tsv
     • ./result/IGLV_freq.tsv
     • ./result/IGV_pair_freq.tsv
     • ./result/HA_Abs_clonotype_public.xlsx

3. Extract IGHD4-17-encoded head antibodies
   python3 script/analyze_IGHD4-17.py

   • Input file:
     • ./doc/HA_Abs_v18.xlsx
   • Output file:
     • ./result/Abs_IGHD4-17.tsv

4. Analyzing the occurrence of YGD motif in CDR H3
   python3 script/analyze_YGD_motif.py

   • Input files:
     • ./doc/HA_Abs_v18.xlsx
     • ./doc/all_paired_antibodies_from_GB_v6.xlsx
   • Ouput file:
     • ./result/YGD_motif_freq.tsv

5. Plot VDJ gene usage
   Rscript script/plot_VDJgene_freq.R

   • Input files:
     • ./result/IGHV_freq.tsv
     • ./result/IGHD_freq.tsv
     • ./result/IGLV_freq.tsv
   • Output files:
     • ./graph/IGHV_usage.png
     • ./graph/IGHD_usage.png
     • ./graph/IGLV_usage.png

6. Plot IGHV/IGK(L)V pairing frequency
   Rscript script/plot_Vpair_heatmap.R

   • Input files:
     • ./result/IGV_pair_freq.tsv
   • Output file:
     • ./graph/Vpair_heatmap.png

7. Plot frequency of YGD motif
   Rscript script/plot_YGD_freq.R

   • Input file:
     • ./result/YGD_motif_freq.tsv
   • Output file:
     • ./graph/YGD_motif_freq.png

mBLM for specificity prediction

See Ab_epitope