Combining DNA and protein alignments to improve genome annotation with LiftOn.
Kuan-Hao ChaoJakob M HeinzCeline HohAlan MaoAlaina ShumateMihaela PerteaSteven L SalzbergPublished in: bioRxiv : the preprint server for biology (2024)
As the number and variety of assembled genomes continues 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 where they exist. LiftOn can reliably transfer annotation between genomes representing members of the same species, as we demonstrate on human, mouse, honey bee, rice, and Arabidopsis thaliana . It can further map annotation effectively across species pairs as far apart as mouse and rat or Drosophila melanogaster and D. erecta .
Keyphrases
- genome wide
- circulating tumor
- rna seq
- arabidopsis thaliana
- cell free
- drosophila melanogaster
- single molecule
- high resolution
- protein protein
- copy number
- endothelial cells
- amino acid
- high density
- dna methylation
- machine learning
- genetic diversity
- binding protein
- single cell
- deep learning
- nucleic acid
- small molecule
- oxidative stress
- induced pluripotent stem cells
- genome wide identification
- circulating tumor cells
- transcription factor