ArticleBMC genomics2018
seq-seq-pan: building a computational pan-genome data structure on whole genome alignment.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Multilocus basis of incipient reproductive isolation in hybridizing populations is revealed by pangenomic and epigenetic divergence.Science advances · 2026Article
- Polygenic basis of incipient reproductive isolation in hybridizing populations is revealed by pangenomic and epigenetic divergence.bioRxiv : the preprint server for biology · 2025Article
- Application of Comparative Genomics for the Development of PCR Primers for the Detection of Harmful or Beneficial Microorganisms in Food: Mini-Review.Foods (Basel, Switzerland) · 2025Review
- Pan-genomics: Insight into the Functional Genome, Applications, Advancements, and Challenges.Current genomics · 2025Review
- Complexity welcome: Pangenome graphs for comprehensive population genomics.Quantitative plant biology · 2025Review
- A gentle introduction to pangenomics.Briefings in bioinformatics · 2024Review
- Speeding genomic island discovery through systematic design of reference database composition.PloS one · 2024Article
- Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon.Nature communications · 2022Article
- A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility.Genome research · 2022Article
- Multiple genome alignment in the telomere-to-telomere assembly era.Genome biology · 2022Review
- Review
- A tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes.BMC bioinformatics · 2021Article
- PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment.Nature communications · 2021Article
- Next-Generation Breeding Strategies for Climate-Ready Crops.Frontiers in plant science · 2021Review
- Improving tuberculosis surveillance by detecting international transmission using publicly available whole genome sequencing data.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2021Article
- Pangenome Graphs.Annual review of genomics and human genetics · 2020Review
- Epidemiological and genetic characterization ofInfection control and hospital epidemiology · 2020Article
- Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters.PLoS computational biology · 2019Article
- Efficient merging of genome profile alignments.Bioinformatics (Oxford, England) · 2019Article
- Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe increasing application of next generation sequencing technologies has led to the availability of thousands of reference genomes, often providing multiple genomes for the same or closely related species. The current approach to represent a species or a population with a single reference sequence and a set of variations cannot represent their full diversity and introduces bias towards the chosen reference. There is a need for the representation of multiple sequences in a composite way that is compatible with existing data sources for annotation and suitable for established sequence analysis methods. At the same time, this representation needs to be easily accessible and extendable to account for the constant change of available genomes.
resultsWe introduce seq-seq-pan, a framework that provides methods for adding or removing new genomes from a set of aligned genomes and uses these to construct a whole genome alignment. Throughout the sequential workflow the alignment is optimized for generating a representative linear presentation of the aligned set of genomes, that enables its usage for annotation and in downstream analyses.
conclusionsBy providing dynamic updates and optimized processing, our approach enables the usage of whole genome alignment in the field of pan-genomics. In addition, the sequential workflow can be used as a fast alternative to existing whole genome aligners for aligning closely related genomes. seq-seq-pan is freely available at https://gitlab.com/rki_bioinformatics.
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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.