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Table 5 Sensitivity and precision of predicted genes after applying different settings

From: Exploiting single-molecule transcript sequencing for eukaryotic gene prediction

Setting Sensitivity in %a Precision in %b
Default A. thaliana parameter set 71.7 42.4
B. vulgaris trained parameter setc 82.3 58.9
+ Hint masking 82.9 62.3
+ Hint masking enforcement 83.6 71.8
+ Additional mRNA-seq hints 76.4 44.6
+ mRNA-seq noise reduction 84.7 73.5
+ Higher weighting of introns 85.0 73.9
+ SMRT reads as anchorsd 91.1 77.9
  1. Settings marked by ‘+’ were added to the setting of the previous line
  2. aPercent of correctly predicted transcripts in the set of SMRT derived test genes not overlapping the training gene set
  3. bPercent of wrongly predicted genes of all correctly and wrongly predicted gene models in genomic regions of SMRT derived test genes
  4. cTraining based on SMRT and manually validated genes
  5. d‘SMRT reads as anchors’ only affected genes covered by SMRT sequences