RATT

RATT transfers annotations from a high-quality reference genome to a query genome by leveraging conserved synteny to propagate gene models, systematic identifiers, and annotator notes for rapid genome annotation.

Key Features:

• Annotation transfer: Transfers gene models, systematic identifiers, and annotator notes from a reference genome to a newly sequenced query genome.
• Conserved synteny-based mapping: Uses preserved gene order between genomes to identify corresponding regions for accurate annotation transfer.
• Preservation of metadata: Retains annotator notes and systematic identifiers during transfer to maintain annotation context.
• Performance: Capable of annotating complex genomes such as Mycobacterium tuberculosis or a 2.5 Mb chromosome from a malaria parasite in under five minutes on modest computational resources.

Scientific Applications:

• Genome annotation: Rapid assignment of gene functions and features across whole genomes.
• Annotation of microbial and parasite genomes: Applied to organisms such as Mycobacterium tuberculosis and malaria parasites for fast re-annotation.
• Large-scale sequencing projects: Facilitates annotation workflows for datasets produced by second-generation sequencing technologies.

Methodology:

RATT detects conserved synteny between reference and query genomes and maps annotation features, including systematic identifiers and annotator notes, from reference regions to corresponding query regions.