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Table 2 Effects of pipeline composition on number of gene predictions and recovery of curated models

From: SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models

  Components in the test pipelines (leftmost is the standard SnowyOwl pipeline)
In Consensus Training Set Orthologs   *   * * * * * * *   
  Contig Models * * *   * * * * * * * *
  GeneMark Models * * * *   * * * * * * *
In Pooled Augustus Models Blat-hinted Models * * * * *   * * * * * *
  Unhinted Models * * * * * *   * * * * *
  Augustus Domains   * * * * * *   * *   
Merged with Pooled Augustus GeneMark Models * * * * * * * *   * *  
  Splice-hinted Models * * * * * * * * *    
  Changes in the number of predicted models relative to the standard pipeline
A. niger Representative (21479) 0 6 61 -8 -21 -9332 12 -61 -27 13 23 -80
  Accepted (11374) 0 24 54 46 15 -1089 20 -35 -60 -5 -21 -149
T. lanuginosus Representative (12915) 0 5 -25 -21 -45 -5367 6 -16 11 5 2 -11
  Accepted (7324) 0 28 13 17 0 -606 26 -7 0 14 -19 -64
P. chrysosporium Representative (20201) 0 92 13 -5742 81 -6444 87 44 52 -56   
  Accepted (12669) 0 111 43 -1585 43 -2058 98 48 48 -87   
  Recovery of curated models (%)
A. niger Representative 94.7 94.7 94.8 94.8 94.8 94.3 94.7 94.8 91.4 91.6 91.6 91.2
  Accepted 94.5 94.5 94.6 94.5 94.5 93.4 94.5 94.5 91.2 91.3 91.3 91.0
T. lanuginosus Representative 93.7 93.8 93.5 93.5 93.7 91.9 93.9 94.0 92.2 92.2 92.3 92.1
  Accepted 93.6 93.7 93.4 93.4 93.6 91.6 93.8 93.9 92.1 92.1 92.2 92.0
P. chrysosporium Representative 88.0 88.1 88.0 90.4 87.8 90.9 88.2 88.2 88.2 84.6   
  Accepted 87.3 87.3 87.1 88.4 87.1 88.5 87.3 87.4 87.4 83.8   
  1. *Component included in pipeline.