ArticleBMC genomics2014
What is the difference between the breakpoint graph and the de Bruijn graph?
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed.
- CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing.Genome research · 2024Article
- CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing.bioRxiv : the preprint server for biology · 2024Article
- Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs.BMC bioinformatics · 2023Article
- KOMB: K-core based de novo characterization of copy number variation in microbiomes.Computational and structural biotechnology journal · 2022Article
- Assembly of long, error-prone reads using repeat graphs.Nature biotechnology · 2019Article
- Chromosome assembly of large and complex genomes using multiple references.Genome research · 2018Article
- Detection and analysis of ancient segmental duplications in mammalian genomes.Genome research · 2018Article
- Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.BMC genomics · 2018Article
- Succinct colored de Bruijn graphs.Bioinformatics (Oxford, England) · 2017Article
- Assembly of long error-prone reads using de Bruijn graphs.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Ancestral gene synteny reconstruction improves extant species scaffolding.BMC genomics · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The breakpoint graph and the de Bruijn graph are two key data structures in the studies of genome rearrangements and genome assembly. However, the classical breakpoint graphs are defined on two genomes (represented as sequences of synteny blocks), while the classical de Bruijn graphs are defined on a single genome (represented as DNA strings). Thus, the connection between these two graph models is not explicit. We generalize the notions of both the breakpoint graph and the de Bruijn graph, and make it transparent that the breakpoint graph and the de Bruijn graph are mathematically equivalent. The explicit description of the connection between these important data structures provides a bridge between two previously separated bioinformatics communities studying genome rearrangements and genome assembly.
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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.