Flanking sequence database of TR alleles from 47 HPRC subjects

This dataset contains flanking sequences of T Cell Receptor (TR) alleles identified from 47 Human Pangenome Reference Consortium (HPRC) subjects. The dataset includes 50 bp and 200 bp flanking sequences for each allele, categorized by gene segment (TRV, TRJ, and TRD).

To facilitate identification, distinct flanking sequences within the same allele are labeled by appending "&flank" to the allele name. Additionally, CSV summary files provide haplotype information (h1 for paternal and h2 for maternal) and the corresponding flanking sequence groups observed in HPRC subjects.

File Descriptions:

FASTA FilesThese files contain the flanking sequences for TR alleles, grouped by allele and categorized by length (50 bp or 200 bp):

TRV_cluster_50.fasta: 50 bp flanking sequences for TRV alleles.

TRV_cluster_200.fasta: 200 bp flanking sequences for TRV alleles.

TRJ_cluster_50.fasta: 50 bp flanking sequences for TRJ alleles.

TRJ_cluster_200.fasta: 200 bp flanking sequences for TRJ alleles.

TRD_cluster_50.fasta: 50 bp flanking sequences for TRD alleles.

TRD_cluster_200.fasta: 200 bp flanking sequences for TRD alleles.

CSV FilesThese files summarize the haplotypes (h1 for paternal and h2 for maternal) observed in the HPRC dataset and the corresponding flanking sequence groupings for each allele:

TRV_cluster_summary_50.csv: Summary of 50 bp flanking sequence groups for TRV alleles.

TRV_cluster_summary_200.csv: Summary of 200 bp flanking sequence groups for TRV alleles.

TRJ_cluster_summary_50.csv: Summary of 50 bp flanking sequence groups for TRJ alleles.

TRJ_cluster_summary_200.csv: Summary of 200 bp flanking sequence groups for TRJ alleles.

TRD_cluster_summary_50.csv: Summary of 50 bp flanking sequence groups for TRD alleles.

TRD_cluster_summary_200.csv: Summary of 200 bp flanking sequence groups for TRD alleles.

The genome assemblies were sourced from the official HPRC GitHub repository:https://github.com/human-pangenomics/HPP_Year1_Assemblies.