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Combining DNA and protein alignments to improve genome annotation with LiftOn
Kuan-Hao Chao1,2, Jakob M Heinz3, Celine Hoh1,2
1Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.
Biorxiv : the Preprint Server for Biology
|May 27, 2024
Summary
LiftOn is a new homology-based software tool that improves genome annotation accuracy by integrating DNA and protein alignments. It enables reliable annotation transfer between even distantly related species.
Area of Science:
- Genomics
- Bioinformatics
- Comparative genomics
Background:
- The rapid expansion of assembled genomes outpaces the rate of genome annotation, especially for eukaryotic organisms.
- Current DNA-based mapping tools are limited to transferring annotations between closely related species.
- Accurate genome annotation is crucial for understanding gene function and evolutionary relationships.
Approach:
- Introduced LiftOn, a novel homology-based software tool for enhanced genome annotation.
- LiftOn integrates both DNA and protein sequence alignments for improved accuracy.
- The protein-centric algorithm optimizes open reading frame selection and resolves gene loci.
Key Points:
- LiftOn successfully transfers genome annotation within species, including human, mouse, honey bee, rice, and Arabidopsis thaliana.
- The tool demonstrates effective annotation mapping between relatively distant species, such as mouse and rat.
- LiftOn can identify additional gene copies and improve the resolution of overlapping gene loci.
Conclusions:
- LiftOn significantly enhances the accuracy and scope of genome-scale annotation.
- This tool facilitates robust annotation transfer across a wider range of species, including those with greater evolutionary divergence.
- LiftOn addresses a critical bottleneck in genomics, enabling more comprehensive analysis of newly assembled genomes.
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