galba

galba predicts protein-coding gene structures in novel eukaryotic genomes using high-quality proteins from closely related species as references.

Key Features:

• Protein-to-genome alignment (miniprot): Uses miniprot, a rapid protein-to-genome aligner, to map reference proteins to target genomes.
• Ab initio gene prediction (AUGUSTUS): Uses AUGUSTUS to infer gene structures informed by protein alignments.
• Reference-driven annotation: Leverages high-quality proteins from closely related species as evidence when transcriptome data are unavailable.
• Automated pipeline: Integrates alignment and prediction steps into an automated workflow for genome-wide annotation.
• Scalability: Demonstrated performance on large vertebrate genomes.
• Cross-taxa applicability: Applied to multiple eukaryotic groups including insects, vertebrates, and land plants.

Scientific Applications:

• Genome annotation without transcriptomes: Predicts protein-coding genes in newly sequenced eukaryotic genomes when RNA-seq or transcriptome data are lacking.
• Vertebrate genome annotation: Annotates large vertebrate genomes using reference proteins and combined miniprot+AUGUSTUS prediction.
• Cross-kingdom eukaryotic annotation: Supports gene structure prediction across taxa such as insects and land plants using reference-driven evidence.

Methodology:

Align reference proteins to the target genome using miniprot and use the resulting alignments as evidence for gene structure prediction with AUGUSTUS within an automated pipeline.