ArticleAlgorithms for molecular biology : AMB2022
Fast characterization of segmental duplication structure in multiple genome assemblies.
Article in Algorithms for molecular biology : AMB, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
44 citing papers in PubMed.
- Telomere-to-telomere genome assembly and a pangenome for the rat.Cell genomics · 2026Article
- Telomere-to-telomere genome assembly of pumpkin (Horticulture research · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Genomes From 117 Vertebrate Species Reveal Rapidly Evolving Segmental-Duplication Landscapes.Genome biology and evolution · 2026Article
- Convergent evolution through independent rearrangements in the primate amylase locus.Cell reports · 2026Article
- Article
- Mapping structural variants in Populus tomentosa reveals adaptive signatures and improves prediction of wood properties.Nature communications · 2026Article
- Chromosome-Scale Genome Architecture and Historical Demography of the Southern White Rhinoceros.Biology · 2026Article
- Diploid dual assemblies reveal the telocentric structure and extensive allelic heterogeneity of canine genomes.NAR genomics and bioinformatics · 2026Article
- Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.Nature communications · 2026Article
- Complete telomere-to-telomere genomes of cowpea reveal insights into centromere evolution in Phaseoleae.Horticulture research · 2026Article
- A pangenome reference and population studies link structural variants with breeding traits in Gossypium hirsutum.Nature genetics · 2026Article
- A phylogenetic estimate of canine retrotransposition rates based on genome assembly comparisons.Mobile DNA · 2026Article
- Single-library chromosome-scale diploid assemblies of vole genomes resolve a species-specific duplication implicated in pair bonding.bioRxiv : the preprint server for biology · 2026Article
- Genomic insights into chromosomal fusion and its evolutionary implications for zokors.Molecular biology and evolution · 2026Article
- The Neijiang pig T2T genome reveals domestication history and germplasm traits of Southwest Chinese local breeds.Communications biology · 2026Article
- SDrecall: a sensitive approach for variant detection in segmental duplications.Genome biology · 2026Article
- Telomere-to-telomere genome assembly of a male pig provides insight into population structure and selection for body stature.Nature genetics · 2026Article
- Chromosome-level assembly and analysis of three hydroxy fatty acid-producing Physaria species.Nature communications · 2025Article
- Near complete assembly of Drosophila melanogaster Canton S strain genome.Nature communications · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
motivationThe increasing availability of high-quality genome assemblies raised interest in the characterization of genomic architecture. Major architectural elements, such as common repeats and segmental duplications (SDs), increase genome plasticity that stimulates further evolution by changing the genomic structure and inventing new genes. Optimal computation of SDs within a genome requires quadratic-time local alignment algorithms that are impractical due to the size of most genomes. Additionally, to perform evolutionary analysis, one needs to characterize SDs in multiple genomes and find relations between those SDs and unique (non-duplicated) segments in other genomes. A naïve approach consisting of multiple sequence alignment would make the optimal solution to this problem even more impractical. Thus there is a need for fast and accurate algorithms to characterize SD structure in multiple genome assemblies to better understand the evolutionary forces that shaped the genomes of today.
resultsHere we introduce a new approach, BISER, to quickly detect SDs in multiple genomes and identify elementary SDs and core duplicons that drive the formation of such SDs. BISER improves earlier tools by (i) scaling the detection of SDs with low homology to multiple genomes while introducing further 7-33[Formula: see text] speed-ups over the existing tools, and by (ii) characterizing elementary SDs and detecting core duplicons to help trace the evolutionary history of duplications to as far as 300 million years. AVAILABILITY AND IMPLEMENTATION: BISER is implemented in Seq programming language and is publicly available at https://github.com/0xTCG/biser .
Indexed as
Identifiers
What OpenQuestion holds
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.