ArticleGenome research2025
Combining DNA and protein alignments to improve genome annotation with LiftOn.
Article in Genome research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed.
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- Chromosomal evolution and speciation inferred from chromosome-scale genome assemblies in three Cupressaceae species.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Genome assemblies and annotations are not static and need support for tracking their evolution.Briefings in bioinformatics · 2026Review
- Tutorial: annotation of animal genomes.Nature protocols · 2026Review
- Chromosome-Scale Genome Architecture and Historical Demography of the Southern White Rhinoceros.Biology · 2026Article
- Two melanic pigment patterns are associated with a sex chromosome-linked oncogene in the mountain swordtailbioRxiv : the preprint server for biology · 2026Article
- Annotating genomes at increased scale and resolution.Nature reviews. Genetics · 2026Review
- AEGIS: an annotation extraction and genomic integration resource.Bioinformatics (Oxford, England) · 2026Article
- Haplotype-resolved telomere-to-telomere assembly and haplotype-aware annotation pipeline enable high-quality reannotation of threeHorticulture research · 2026Article
- Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomes.BMC genomics · 2026Article
- Haplotype-resolved genome sequences of a springtail species, Folsomia candida (Collembola: Isotomidae).Scientific data · 2026Article
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- Time-Efficient and Informatic-Skill-Light Gap-Filling for Telomere-to-Telomere Genome Assembly.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A neofunctionalized flowering antagonist created an evolutionary contingency that channeled Solanaceae adaptation.bioRxiv : the preprint server for biology · 2026Article
- De Novo Assembly of Eight Commercial Crossbred Pig Genomes Provides Insights into the Potential Functional Impact of Structural Variation Hotspots.Biomolecules · 2026Article
- Intraspecies sequence-graph analysis of the Phytophthora theobromicola genome reveals a dynamic structure and variable effector repertoires.G3 (Bethesda, Md.) · 2026Article
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- JoGo 1.0: the ACTG hierarchical nomenclature and database covering 4.7 million haplotypes across 19,194 human genes.Nucleic acids research · 2026Article
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Abstract
As the number and variety of assembled genomes continue to grow, the number of annotated genomes is falling behind, particularly for eukaryotes. DNA-based mapping tools help to address this challenge, but they are only able to transfer annotation between closely related species. Here we introduce LiftOn, a homology-based software tool that integrates DNA and protein alignments to enhance the accuracy of genome-scale annotation and to allow mapping between relatively distant species. LiftOn's protein-centric algorithm considers both types of alignments, chooses optimal open reading frames, resolves overlapping gene loci, and finds additional gene copies when they exist. LiftOn can reliably transfer annotation between genomes representing members of the same species, as we demonstrate on human, mouse, honeybee, rice, and
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