CATEGORY 1
----------

/fml/ag-raetsch/share/projects/nGASP/LSL/cat-1/test_predictions/gr_final_linear-30-12-2006G3A_gene_predictions_category1_V1_Jan_01_2007.gff

cat-1 (lp)
cleave_offset = 2.5
iteration 18

Evaluating predictions from /fml/ag-raetsch/share/projects/nGASP/LSL/cat-1/predictions/gr_final_linear-30-12-2006/pred_split=5_cleave2.50.mat...
(CONFIRMED)
  processed 247 blocks

Evaluation
  on nucleotide level:
    sensitivity: 97.46%
    specificity: 97.41%

  on coding exon level:
    sensitivity: 90.65% (missing exons: 3.96%)
    specificity: 92.26% (wrong exons:   2.26%)

  on transcript level:
    sensitivity: 59.81%
    specificity: 79.01%

(UNCONFIRMED)
  processed 247 blocks

Evaluation
  on nucleotide level:
    sensitivity: 91.22%
    specificity: 88.50%

  on coding exon level:
    sensitivity: 78.60% (missing exons: 7.33%)
    specificity: 73.36% (wrong exons:   13.06%)

  on transcript level:
    sensitivity: 38.25%
    specificity: 37.56%

(ALL)
  processed 247 blocks

Evaluation
  on nucleotide level:
    sensitivity: 92.30%
    specificity: 89.99%

  on coding exon level:
    sensitivity: 80.98% (missing exons: 6.65%)
    specificity: 76.91% (wrong exons:   10.98%)

  on transcript level:
    sensitivity: 42.88%
    specificity: 42.50%

V3 with alternative splicing:
/fml/ag-raetsch/share/projects/nGASP/LSL/cat-1/test_predictions/gr_final_linear-30-12-2006/G3A_gene_predictions_category1_V3_Jan_01_2007.gff

CATEGORY 2
----------

cat-2 V1
/fml/ag-raetsch/share/projects/nGASP/LSL/cat-2/test_predictions/gr_final_linear-30-12-2006G3A_gene_predictions_category2_V1_Jan_01_2007.gff
cleave_offset=4.0
(about from iteration 13)

cat-2 V2
/fml/ag-raetsch/share/projects/nGASP/LSL/cat-2/test_predictions/gr_con_final-30-12-2006/G3A_gene_predictions_category2_V2_Jan_01_2007.gff

cat-2 V1a
/fml/ag-raetsch/share/projects/nGASP/LSL/cat-2/test_predictions/gr_final_linear-30-12-2006G3A_gene_predictions_category2_V1_Jan_01_2007.gff
cleave_offset=3.5
(iteration 26 or so)

Evaluating predictions from
/fml/ag-raetsch/share/projects/nGASP/LSL/cat-2/predictions/gr_con_final-30-12-2006/pred_split=5_cleave3.50.mat...
(CONFIRMED)
  processed 151 blocks

Evaluation
  on nucleotide level:
    sensitivity: 98.49%
    specificity: 96.05%

  on coding exon level:
    sensitivity: 92.07% (missing exons: 1.83%)
    specificity: 90.60% (wrong exons:   3.40%)

  on transcript level:
    sensitivity: 61.90%
    specificity: 74.29%

(UNCONFIRMED)
  processed 151 blocks

Evaluation
  on nucleotide level:
    sensitivity: 92.11%
    specificity: 87.72%

  on coding exon level:
    sensitivity: 79.93% (missing exons: 6.78%)
    specificity: 73.77% (wrong exons:   13.60%)

  on transcript level:
    sensitivity: 41.15%
    specificity: 36.10%

(ALL)
  processed 151 blocks

Evaluation
  on nucleotide level:
    sensitivity: 93.53%
    specificity: 89.54%

  on coding exon level:
    sensitivity: 82.88% (missing exons: 5.57%)
    specificity: 77.77% (wrong exons:   11.12%)

  on transcript level:
    sensitivity: 48.25%
    specificity: 43.54%


CATEGORY 3
----------

/fml/ag-raetsch/share/projects/nGASP/LSL/cat-3/test_predictions/gr_final_linear-30-12-2006G3A_gene_predictions_category3_V1_Jan_01_2007.gff

cat-3 (lp) V1
cleave_offset = 2.5
iteration 18 (cat-1)

Evaluating predictions from /fml/ag-raetsch/share/projects/nGASP/LSL/cat-3/predictions/gr_final_linear-30-12-2006/pred_split=5_cleave2.50.mat...
(CONFIRMED)
  processed 247 blocks

Evaluation
  on nucleotide level:
    sensitivity: 99.11%
    specificity: 98.48%

  on coding exon level:
    sensitivity: 95.74% (missing exons: 1.58%)
    specificity: 95.74% (wrong exons:   1.58%)

  on transcript level:
    sensitivity: 78.50%
    specificity: 95.45%

(UNCONFIRMED)
  processed 247 blocks

Evaluation
  on nucleotide level:
    sensitivity: 91.82%
    specificity: 88.61%

  on coding exon level:
    sensitivity: 80.84% (missing exons: 6.14%)
    specificity: 74.71% (wrong exons:   12.86%)

  on transcript level:
    sensitivity: 43.78%
    specificity: 41.94%

(ALL)
  processed 247 blocks

Evaluation
  on nucleotide level:
    sensitivity: 93.08%
    specificity: 90.27%

  on coding exon level:
    sensitivity: 83.80% (missing exons: 5.21%)
    specificity: 78.66% (wrong exons:   10.70%)

  on transcript level:
    sensitivity: 51.60%
    specificity: 49.83%


 /fml/ag-raetsch/share/projects/nGASP/LSL/cat-3/test_predictions/gr_final_linear-30-12-2006G3A_gene_predictions_category3_V2_Jan_01_2007.gff

cat-3 (lp) V2
cleave_offset = 5.0
iteration 18 (cat-1)

Evaluating predictions from /fml/ag-raetsch/share/projects/nGASP/LSL/cat-3/predictions/gr_final_linear-30-12-2006/pred_split=5_cleave5.00.mat...
(CONFIRMED)
  processed 247 blocks

Evaluation
  on nucleotide level:
    sensitivity: 99.39%
    specificity: 97.92%

  on coding exon level:
    sensitivity: 96.37% (missing exons: 1.10%)
    specificity: 95.02% (wrong exons:   2.49%)

  on transcript level:
    sensitivity: 81.31%
    specificity: 93.55%

(UNCONFIRMED)
  processed 247 blocks

Evaluation
  on nucleotide level:
    sensitivity: 95.09%
    specificity: 83.56%

  on coding exon level:
    sensitivity: 80.94% (missing exons: 4.31%)
    specificity: 68.52% (wrong exons:   18.62%)

  on transcript level:
    sensitivity: 45.85%
    specificity: 31.05%

(ALL)
  processed 247 blocks

Evaluation
  on nucleotide level:
    sensitivity: 95.84%
    specificity: 85.82%

  on coding exon level:
    sensitivity: 84.00% (missing exons: 3.65%)
    specificity: 73.23% (wrong exons:   15.70%)

  on transcript level:
    sensitivity: 53.56%
    specificity: 38.79%


/fml/ag-raetsch/share/projects/nGASP/LSL/cat-3/test_predictions/gr_final_linear-30-12-2006/G3A_gene_predictions_category3_V3_Jan_01_2007.gff
V3 (alternative splicing), sonst wie V1

ID_cnt =

             id_len: 7
    current_gene_id: 1845
    current_mrna_id: 1928
    current_exon_id: 13082
     current_cds_id: 12962
