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Table 2 Performance comparison of gene prediction tools on A. thaliana with the transition probabilities trained by computing maximum likelihood estimation

From: GPRED-GC: a Gene PREDiction model accounting for 5 - 3 GC gradient

Program

 

AUGUSTUS

GPRED-GC

   

lowT=0.47

lowT=0.30

lowT=0.30

lowT=0.60

   

highT=0.63

highT=0.60

highT=0.70

highT=0.70

Base

Sen

0.968

0.960

0.972

0.972

0.972

level

Spe

0.708

0.711

0.709

0.709

0.709

Exon

Sen

0.870

0.851

0.882

0.882

0.882

level

Spe

0.666

0.674

0.677

0.677

0.677

Gene

Sen

0.554

0.560

0.565

0.565

0.565

level

Spe

0.352

0.346

0.351

0.351

0.351

Time(Sec.)

 

40.3

51.1

57.7

56.4

57.7

  1. The two tools have comparable performance. Time (Sec.) is the running time of AUGUSTUS and GPRED-GC under different sets of thresholds on A. thaliana dataset in seconds. Note: The running time represents the total running time of prediction