ArticleBioinformatics (Oxford, England)2021
d-PBWT: dynamic positional Burrows-Wheeler transform.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- An Efficient Dynamic Data Structure for Haplotype Matching and Compression on Biobank-Scale Data.Journal of computational biology : a journal of computational molecular cell biology · 2026Article
- FRAME: fast reference-based ancestry makeup estimation tool.Bioinformatics advances · 2026Article
- Sparse haplotype-based fine-scale local ancestry inference at scale reveals recent selection on immune responses.Nature communications · 2025Article
- DynamicbioRxiv : the preprint server for biology · 2025Article
- Haplotype Matching with GBWT for Pangenome Graphs.bioRxiv : the preprint server for biology · 2025Article
- An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2025Article
- Discovery of runs-of-homozygosity diplotype clusters and their associations with diseases in UK Biobank.eLife · 2024Article
- μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data.Bioinformatics (Oxford, England) · 2023Article
- Minimal positional substring cover is a haplotype threading alternative to Li and Stephens model.Genome research · 2023Article
- RaPID-Query for fast identity by descent search and genealogical analysis.Bioinformatics (Oxford, England) · 2023Article
- Minimal Positional Substring Cover: A Haplotype Threading Alternative to Li & Stephens Model.bioRxiv : the preprint server for biology · 2023Article
- Exploiting parallelization in positional Burrows-Wheeler transform (PBWT) algorithms for efficient haplotype matching and compression.Bioinformatics advances · 2023Article
- Syllable-PBWT for space-efficient haplotype long-match query.Bioinformatics (Oxford, England) · 2023Article
- Haplotype Threading Using the Positional Burrows-Wheeler Transform.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2022Article
- Discovery of runs-of-homozygosity diplotype clusters and their associations with diseases in UK Biobank.medRxiv : the preprint server for health sciences · 2020Article
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Authors and funding
3 authors.
Funding
Abstract
motivationDurbin's positional Burrows-Wheeler transform (PBWT) is a scalable data structure for haplotype matching. It has been successfully applied to identical by descent (IBD) segment identification and genotype imputation. Once the PBWT of a haplotype panel is constructed, it supports efficient retrieval of all shared long segments among all individuals (long matches) and efficient query between an external haplotype and the panel. However, the standard PBWT is an array-based static data structure and does not support dynamic updates of the panel.
resultsHere, we generalize the static PBWT to a dynamic data structure, d-PBWT, where the reverse prefix sorting at each position is stored with linked lists. We also developed efficient algorithms for insertion and deletion of individual haplotypes. In addition, we verified that d-PBWT can support all algorithms of PBWT. In doing so, we systematically investigated variations of set maximal match and long match query algorithms: while they all have average case time complexity independent of database size, they have different worst case complexities and dependencies on additional data structures. AVAILABILITYAND IMPLEMENTATION: The benchmarking code is available at genome.ucf.edu/d-PBWT. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.