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Table 2 Genome-wide assessment of ab initio gene prediction methods

From: A draft annotation and overview of the human genome

Genscan

Grail

Fgenes

Transcript-

Protein-

Unconfirmed

   

confirmed

supported

exons

   

exons

exons

 

  

25,619

2,890

45,025

 

 

52,644

14,685

434,409

  

7,791

796

257,676

 

17,841

3,761

28,556

  

13,915

1,711

11,628

 

3,990

450

49,420

53,566

9,871

20,569

Total exons

  

175,366

34,164

847,283

  1. Three gene prediction programs, Genscan [93], Fgenes [94] and Grail1.3 [95] were used to screen individual genomic contigs. Exons consistently predicted by more than one program are merged into a unique exon index, which is then compared to transcript- and protein-based exons in complete ORFs. Transcript-confirmed exons, overlapping of predicted exons with transcript-based exons; protein-supported exons, predicted exons have at least strong protein homology (E < 10-15); unconfirmed exons, predicted exons have no overlap with transcripts nor protein homology.