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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

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Published on: August 15, 2019

Liftoff: accurate mapping of gene annotations.

Alaina Shumate^1,2, Steven L Salzberg^1,2,3,4

¹Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.

Bioinformatics (Oxford, England)

|December 15, 2020

Summary

Liftoff is a new tool that accurately maps genes between genome assemblies. It successfully transfers gene annotations from reference genomes to new assemblies, even across species, preserving gene structure and sequence identity.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Advancements in DNA sequencing and computational methods have increased the availability of high-quality genome assemblies.
Accurate gene annotation is crucial for understanding genome biology, but is often limited to reference genomes.

Purpose of the Study:

To introduce Liftoff, a novel tool for genome annotation transfer (lift-over).
To enable efficient and accurate mapping of genes between different genome assemblies.

Main Methods:

Liftoff aligns genes from a reference genome to a target genome.
The tool optimizes mapping by maximizing sequence identity while preserving exon, transcript, and gene structure.

Main Results:

Liftoff accurately mapped 99.9% of genes between human reference genome versions with >99.9% sequence identity.
The tool successfully transferred 98.3% of human protein-coding genes to a chimpanzee assembly with 98.2% sequence identity.

Conclusions:

Liftoff provides a highly accurate and efficient method for transferring gene annotations between genome assemblies.
This tool facilitates the annotation of newly assembled genomes, including cross-species applications.