Table 3.

Exon Level Per Transcript-Pair Comparison to Manual Annotations

	Exact pairs	Sn	Sp	Exact pairs (coding)	Sn (coding)	Sp (coding)
chr13	82%	0.73	0.78	93%	0.83	0.90
chr14	80%	0.69	0.77	90%	0.78	0.88
chr6	80%	0.73	0.76	92%	0.85	0.89

Only exons that are part of a transcript-pair are compared with each other. An annotated exon is considered found if there is at least one predicted exon with exact matching boundaries in a given transcript-pair. The second and fourth columns give the percentage of exact exon matches from the total number of exon-pairs formed within the transcript-pairs for all-exons and for coding exons, respectively. The sensitivity and specificity values are also given. The values are higher for coding exons, which indicates that UTR annotation remains a difficult problem.