domains / families / science / eukaryotic-gene-prediction

eukaryotic-gene-prediction

separate

Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate (fungi), GeMoMa (homology projection), or Helixer/Tiberius (deep-learning ab initio). Covers the evidence-first tool decision, mandatory soft-masking, the training-set-quality-dominates principle, OrthoDB clade-partition selection, the one-isoform-per-locus and missing-UTR traps, merge/split errors, and reference bias against orphan genes. Use when annotating a newly assembled eukaryotic genome, choosing a gene-prediction pipeline based on available evidence, or diagnosing a poor annotation.

When to use

• annotating a newly assembled eukaryotic genome
• choosing a gene-prediction pipeline based on available evidence
• diagnosing a poor annotation
• identifying protein-coding gene structures
• training gene finders with RNA-seq and protein evidence

When not to use

• prokaryotic gene prediction
• non-protein-coding gene prediction
• assembly decontamination
• assembly contiguity checking

Skill page

Source