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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.