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Updated: Jun 18, 2026
07:08
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Combining DNA and protein alignments to improve genome annotation with LiftOn
Kuan-Hao Chao1,2, Jakob M Heinz3, Celine Hoh4,2
1Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA; kh.chao@cs.jhu.edu salzberg@jhu.edu.
Genome Research
|December 27, 2024
Summary
LiftOn is a new homology-based tool that improves genome annotation accuracy by integrating DNA and protein alignments. This software enables reliable annotation transfer between even distantly related species.
Area of Science:
- Genomics
- Bioinformatics
- Comparative Genomics
Background:
- The increasing number of assembled genomes outpaces annotation efforts, especially for eukaryotes.
- Current DNA-based mapping tools have limitations in transferring annotations between distantly related species.
Purpose of the Study:
- To introduce LiftOn, a novel homology-based software tool for enhancing genome-scale annotation accuracy.
- To enable reliable annotation transfer between relatively distant species by integrating diverse alignment data.
Main Methods:
- LiftOn utilizes a protein-centric algorithm that combines DNA and protein alignments.
- The tool optimizes open reading frame selection and resolves overlapping gene loci.
- It identifies additional gene copies to improve annotation completeness.
Main Results:
- LiftOn demonstrated reliable annotation transfer within species, including human, mouse, honeybee, rice, and Arabidopsis thaliana.
- Effective annotation mapping was achieved across distant species pairs, such as mouse and rat, and Drosophila melanogaster and Drosophila erecta.
Conclusions:
- LiftOn significantly enhances the accuracy and scope of genome annotation transfer.
- The tool's ability to bridge annotation gaps between diverse species represents a major advancement in comparative genomics.
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