LiftOn

LiftOn integrates DNA-DNA and protein-DNA alignments to improve genome annotation accuracy and enable homology-based lift-over between genomes, including relatively distant eukaryotic species.

Key Features:

• Dual-alignment integration: LiftOn combines DNA-DNA and protein-DNA alignments to maximize protein-coding gene annotation accuracy.
• Optimal open reading frame selection: The protein-centric algorithm chooses optimal open reading frames from both alignment types.
• Overlapping gene locus resolution: LiftOn resolves overlapping gene loci during annotation transfer.
• Additional gene copy detection: The tool finds additional gene copies when they exist in the target genome.
• Cross-species mapping capability: LiftOn enables annotation transfer between relatively distant species, demonstrated on pairs including mouse and rat and Drosophila melanogaster and Drosophila erecta.

Scientific Applications:

• Eukaryotic genome annotation: LiftOn addresses the growing gap between assembled and annotated eukaryotic genomes by enabling accurate annotation transfer.
• Same-species annotation transfer: The tool reliably transfers annotation between genomes of the same species, demonstrated on human, mouse, honeybee, rice, and Arabidopsis thaliana.
• Cross-species annotation mapping: LiftOn maps annotation effectively across species pairs that are too distant for DNA-based mapping tools alone.

Methodology:

LiftOn uses a protein-centric algorithm that considers both DNA and protein alignments, chooses optimal open reading frames, resolves overlapping gene loci, and finds additional gene copies when they exist.