biostudies-literatureChao KHNHGRI NIH HHSNIGMS NIH HHS311-325https://www.ebi.ac.uk/biostudies/studies/S-EPMC11874971biostudies-literatureUnknown35(2)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 humGenome researchCombining DNA and protein alignments to improve genome annotation with LiftOn.PMC11874971R01 HG006677T32 HG002295R35 GM130151Mao AShumate AHeinz JMChao KHSalzberg SLPertea MHoh CfalseCombining DNA and protein alignments to improve genome annotation with LiftOn.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 hum2025-01-01T00:00:00Z2025 Feb2026-03-18T13:28:38.12Z2025-08-18T09:54:20.93ZS-EPMC118749713973018810.1101/gr.279620.124