Liftoff

Liftoff maps gene annotations from a well-annotated reference genome to new or improved target genome assemblies to transfer exon, transcript, and gene features across the same or closely related species.

Key Features:

• Gene Mapping Across Assemblies: Maps genes between two genome assemblies of the same species, transferring gene features and other functional elements to the target assembly.
• Cross-Species Annotation Transfer: Transfers annotations across closely-related species to enable comparative annotation between assemblies from different taxa.
• Maximized Sequence Identity with Structural Preservation: Aligns genes by maximizing sequence identity while preserving the structural integrity of exons, transcripts, and genes.
• High Accuracy and Performance: Demonstrated mapping of 99.9% of genes between two versions of the human reference genome with an average sequence identity exceeding 99.9%, and mapping of 98.4% of human protein-coding genes to a chimpanzee genome assembly with 98.7% sequence identity.

Scientific Applications:

• Genome annotation transfer: Enables annotation of new or improved assemblies by transferring existing reference annotations rather than annotating de novo.
• Comparative genomics: Facilitates cross-species and within-species comparisons of gene content and structure between assemblies.
• Functional and evolutionary genomics: Supports functional genomics and evolutionary biology studies that require accurate gene models across assemblies.

Methodology:

Liftoff aligns genes from a reference genome to a target genome assembly using an alignment algorithm that maximizes sequence identity while preserving the structural integrity of exons, transcripts, and genes.