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. 2014 Jul 1;15:229. doi: 10.1186/1471-2105-15-229

Table 2.

Effects of pipeline composition on number of gene predictions and recovery of curated 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    

*Component included in pipeline.