ArticleNature methods2023
UniAligner: a parameter-free framework for fast sequence alignment.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 21 citations in OpenAlex.
- AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates.Bioinformatics (Oxford, England) · 2026Article
- Efficient sequence alignment against millions of prokaryotic genomes with LexicMap.Nature biotechnology · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- MGA: a tool for haplotype-mixed assembly of long and accurate reads.Genome biology · 2026Article
- mm2-ivh: simple and precise overlap detection in alpha satellite HORs with interval hashing.Bioinformatics (Oxford, England) · 2026Article
- HAlign-G: rapid and low-memory multiple-genome aligner for large-scale closely related genomes.Genome biology · 2025Article
- Minimizing detection bias of somatic mutations in a highly heterozygous oak genome.G3 (Bethesda, Md.) · 2025Article
- A draft UAE-based Arab pangenome reference.Nature communications · 2025Article
- Fast sequence alignment for centromeres with RaMA.Genome research · 2025Article
- GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions.Bioinformatics (Oxford, England) · 2025Article
- Advances in Whole Genome Sequencing: Methods, Tools, and Applications in Population Genomics.International journal of molecular sciences · 2025Review
- ModDotPlot-rapid and interactive visualization of tandem repeats.Bioinformatics (Oxford, England) · 2024Article
- Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References.Annual review of genomics and human genetics · 2024Review
- ModDotPlot-Rapid and interactive visualization of complex repeats.bioRxiv : the preprint server for biology · 2024Article
- Envisioning a new era: Complete genetic information from routine, telomere-to-telomere genomes.American journal of human genetics · 2023Review
- A survey of mapping algorithms in the long-reads era.Genome biology · 2023Review
- The variation and evolution of complete human centromeres.bioRxiv : the preprint server for biology · 2023Article
- Review
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Even though the recent advances in 'complete genomics' revealed the previously inaccessible genomic regions, analysis of variations in centromeres and other extra-long tandem repeats (ETRs) faces an algorithmic challenge since there are currently no tools for accurate sequence comparison of ETRs. Counterintuitively, the classical alignment approaches, such as the Smith-Waterman algorithm, fail to construct biologically adequate alignments of ETRs. We present UniAligner-the parameter-free sequence alignment algorithm with sequence-dependent alignment scoring that automatically changes for any pair of compared sequences. UniAligner prioritizes matches of rare substrings that are more likely to be relevant to the evolutionary relationship between two sequences. We apply UniAligner to estimate the mutation rates in human centromeres, and quantify the extremely high rate of large duplications and deletions in centromeres. This high rate suggests that centromeres may represent some of the most rapidly evolving regions of the human genome with respect to their structural organization.
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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.