ArticleProceedings of the National Academy of Sciences of the United States of America2022
AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 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
71 citing papers in PubMed.
- The MexMAGIC population reveals the genetic architecture of traits exhibiting clinal variation in Mexican native maize.The New phytologist · 2026Article
- Article
- PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants.Cell genomics · 2026Article
- Advances in genomics-driven genetic decoding and genomic design breeding in tomato.Horticulture research · 2026Article
- Balanced polymorphism in a floral transcription factor underlies the ancient rhythm of daily sex alternation in avocado.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A pangenome of tetraploid wheat reveals the genetic architecture underlying domestication and genomic diversity for breeding.Nature genetics · 2026Article
- The hidden sources of spurious fusion transcripts in plants.Genome biology · 2026Article
- The genetic control of rapid genome content divergence inbioRxiv : the preprint server for biology · 2026Article
- Pangenomics for Agricultural Breeding: Construction Strategies, Evidence Integration, and Translational Constraints.Biology · 2026Review
- Rapid centromere turnover and the adaptive radiation of lemurs.bioRxiv : the preprint server for biology · 2026Article
- Singletrack: an algorithm for improving memory consumption and performance of gap-affine sequence alignment.Bioinformatics (Oxford, England) · 2026Article
- The relationship between genomic variation and genetic load: insights from small island populations.Heredity · 2026Article
- Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon.Nature genetics · 2026Article
- Chromatin accessibility landscape and its association with heterosis in maize hybrids.Nature communications · 2026Article
- quota_Anchor: a strand and whole genome duplication-aware collinear gene identification tool.aBIOTECH · 2026Article
- Accelerating minimap2 for whole-genome alignment.Bioinformatics (Oxford, England) · 2026Article
- Near-complete genome assembly of a transformation-efficient elite inbred line LH244 and its comparison with B73.Journal of integrative plant biology · 2026Article
- Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize.Genome research · 2026Article
- Widespread turnover of a conserved cis-regulatory code across 589 grass species.Molecular biology and evolution · 2026Article
- Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado.bioRxiv : the preprint server for biology · 2025Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Millions of species are currently being sequenced, and their genomes are being compared. Many of them have more complex genomes than model systems and raise novel challenges for genome alignment. Widely used local alignment strategies often produce limited or incongruous results when applied to genomes with dispersed repeats, long indels, and highly diverse sequences. Moreover, alignment using many-to-many or reciprocal best hit approaches conflicts with well-studied patterns between species with different rounds of whole-genome duplication. Here, we introduce Anchored Wavefront alignment (AnchorWave), which performs whole-genome duplication-informed collinear anchor identification between genomes and performs base pair-resolved global alignment for collinear blocks using a two-piece affine gap cost strategy. This strategy enables AnchorWave to precisely identify multikilobase indels generated by transposable element (TE) presence/absence variants (PAVs). When aligning two maize genomes, AnchorWave successfully recalled 87% of previously reported TE PAVs. By contrast, other genome alignment tools showed low power for TE PAV recall. AnchorWave precisely aligns up to three times more of the genome as position matches or indels than the closest competitive approach when comparing diverse genomes. Moreover, AnchorWave recalls transcription factor-binding sites at a rate of 1.05- to 74.85-fold higher than other tools with significantly lower false-positive alignments. AnchorWave complements available genome alignment tools by showing obvious improvement when applied to genomes with dispersed repeats, active TEs, high sequence diversity, and whole-genome duplication variation.
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.