Augustus Genes (BUSCO) Track Settings

Augustus Gene Predictions with BUSCO Training Set (All Gene Predictions (Species-specific Parameters) tracks)

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Data last updated at UCSC: 2022-10-20

Description

This track shows the gene models from the Augustus gene predictor using the species-specific parameters estimated from a training set produced by BUSCO.

Methods

The training set used to estimate the species-specific parameters for the Augustus analysis was produced by BUSCO using the arthropoda_odb9 dataset.

Transposons remnants identified by RepeatMasker were provided as hints to the Augustus gene predictor. The following additional parameters were used with the Augustus gene predictor:

  --strand=both
  --noInFrameStop=true
  --gff3=on
  --uniqueGeneId=true
  --protein=off
  --codingseq=off
  --introns=off
  --stop=off
  --cds=on
  --singlestrand=false
  --UTR=off
  --genemodel=partial

References

Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25.

Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015 Oct 1;31(19):3210-2.