domains / families / science / annotation-transfer

annotation-transfer

separate

Transfers gene annotations between genome assemblies via coordinate liftover (UCSC liftOver, CrossMap for same-species version updates) or feature/sequence projection (Liftoff for same/close species, miniprot for protein-level cross-species, TOGA/GeMoMa/CAT for distant clades). Covers the coordinate-vs-projection decision by divergence, why a successful lift is not biological confirmation, reference bias, the silent-dropping of unmapped features, build/PAR/MHC/inversion hazards, and transfer-vs-de-novo validation. Use when annotating a new assembly of a species with an existing reference, harmonizing coordinates across builds, or mapping annotations across related species.

When to use

• annotating a new assembly of a species with an existing reference
• harmonizing coordinates across builds
• mapping annotations across related species
• same-species version updates
• variant/peak/CNV harmonization
• cross-assembly/species gene model transfer
• polyploid/duplicated genome annotation

When not to use

• de novo gene prediction for distant clades
• calling gene gain
• cross-species coordinate liftover

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