DOI: 10.5281/zenodo.15931791
title: Data for: A sitewise model of natural selection on individual antibodies via a transformer-encoder

description: This record provides processed B-cell receptor (BCR) data from various studies as described in Matsen IV, F. et al. (2025). A sitewise model of natural selection on individual antibodies via a transformer-encoder. Molecular Biology and Evolution. The software to reproduce the results in that publication can be found here.

BCR sequences are clustered into clonal families and germline sequences are inferred. For each clonal family, phylogenetic tree inference and reconstruction of ancestral sequences are performed. The parent and child sequences of each branch of a tree form a "parent-child pair" (PCP), which are used for training or evaluating models. Only heavy chain sequences are considered in this work.

 

PCP data files

The dnsm_data.tar.gz contains dataframes of PCP from various datasets and simulations.

Processed datasets are found in the DATA_DIR/v3/ directory:




file name
description


wyatt-10x-1p5m_fs-all-NoWinCheck_igh_pcp_2024-10-29_NI_noN_no-naive.csv.gz
PCPs of BCR sequences from Jaffe et al. (2022).


tang-deepshm-prod-NoWinCheck_igh_pcp_2024-10-29_MASKED_NI_noN_no-naive.csv.gz
PCPs of BCR sequences from Tang et al. (2022) and Vergani et al. (2017).


rodriguez-airr-seq-race-prod-NoWinCheck_igh_pcp_2024-11-12_MASKED_NI_noN_no-naive.csv.gz
PCPs of BCR sequences from Rodriguez et al. (2023).




Corresponding per clonal familiy IMGT numbering schemes for each dataset are found in DATA_DIR/v3/anarci/.

Simulation datasets are found in the DATA_DIR/simulations/v3/ directory:




file name
description


v3convert_dnsm_jaffe+tang_SIM_rodriguez-6-2-25_NI_no-naive.csv.gz
PCPs from simulation of BCR sequences along trees inferred from Rodriguez et al. (2023).


v3convert_dnsm_jaffe+tang_SIM_v2tang-2025-6-3_NI_no-naive_CONCAT_dnsm_jaffe+tang_SIM_v1jaffebulk-2025-6-3_NI_no-naive.csv.gz
PCPs from simulation of BCR sequences along trees inferred from Jaffe et al. (2022), and Tang et al. (2022) and Vergani et al. (2017).


v3convert_dnsm_jaffe+tang_SIM_v2tang-2025-6-3_NI_no-naive_CONCAT_dnsm_jaffe+tang_SIM_v1jaffebulk-2025-6-3_NI_no-naive_downsample_50k.csv.gz


50k subset of PCPs from simulation along trees inferred from Jaffe et al. (2022), and Tang et al. (2022) and Vergani et al. (2017).



v3convert_dnsm_jaffe+tang_SIM_v2tang-2025-6-3_NI_no-naive_CONCAT_dnsm_jaffe+tang_SIM_v1jaffebulk-2025-6-3_NI_no-naive_downsample_100k.csv.gz
100k subset of PCPs from simulation along trees inferred from Jaffe et al. (2022), and Tang et al. (2022) and Vergani et al. (2017).


v3convert_dnsm_jaffe+tang_SIM_v2tang-2025-6-3_NI_no-naive_CONCAT_dnsm_jaffe+tang_SIM_v1jaffebulk-2025-6-3_NI_no-naive_downsample_250k.csv.gz
250k subset of PCPs from simulation along trees inferred from Jaffe et al. (2022), and Tang et al. (2022) and Vergani et al. (2017).




 

PCP data format




column
description


sample_id
sample label, where a sample corresponds to an individual


family
clonal family label within a sample


parent_name
label of the parent sequence


parent_heavy
parent heavy chain sequence


child_name
label of the child sequence


child_heavy
child heavy chain sequence


branch_length
branch length computed in IQ-TREE


depth
the number of edges that the child sequence is away from the naive sequence in the inferred tree


distance
sum of branch lengths from the naive sequence to the child sequence


v_gene_heavy
inferred heavy chain V gene


j_gene_heavy
inferred heavy chain J gene


cdr1_codon_start_heavy
position of the first nucleotide of the first codon in heavy chain CDR1


cdr1_codon_end_heavy
position of the first nucleotide of the last codon in heavy chain CDR1


cdr2_codon_start_heavy
position of the first nucleotide of the first codon in heavy chain CDR2


cdr2_codon_end_heavy
position of the first nucleotide of the last codon in heavy chain CDR2


cdr3_codon_start_heavy
position of the first nucleotide of the first codon in heavy chain CDR3


cdr3_codon_end_heavy
position of the first nucleotide of the last codon in heavy chain CDR3


parent_is_naive
True/False whether the parent sequence is the naive sequence of the clonal family


child_is_leaf
True/False whether the child sequence is a leaf node of the tree


rate_scale_heavy
Correction factor for the heavy chain evolution rate (simulation files only, but not used in the analysis)


rate_scale_light
Correction factor for the light chain evolution rate (simulation files only, but not used in the analysis)