AceView: a comprehensive cDNA-supported gene and transcripts annotation

Table 2 Sensitivity and specificity of each method at detecting the 1,556 consensus transcripts

Track	Number of models with introns	Consensual models (of 1,556 total)	Sensitivity	Specificity
*AceView	1,792	1,302	84%	73%
Gencode	1,691	1,255	81%	74%
*ECgene	3,851	1,198	77%	31%
AceView	1,630	1,165	75%	71%
*ExonWalk	892	511	33%	57%
*Known Gene	501	432	28%	86%
Exogean	554	404	26%	73%
*RefSeq	342	332	21%	97%
Pairagon	471	310	20%	66%
*Ensembl	427	295	19%	69%
*MGC	323	217	14%	67%
Fgenesh	462	217	14%	47%
*P CCDS	201	152	10%	76%
UP Jigsaw	259	150	10%	58%
*U NscanEst	282	104	7%	37%
UP Augustus	312	100	6%	32%
P Twinscan	547	77	5%	14%
UP GeneMark	551	50	3%	9%
UP SGP2	552	48	3%	9%
UP GeneZilla	477	47	3%	10%
UP ExonHunter	807	41	3%	5%
UP GeneID	267	38	2%	14%
*UP GenScan	395	37	2%	9%
UP Dogfish	204	33	2%	16%
UP Saga	331	18	1%	5%

Sensitivity and specificity of each method at detecting the 1,556 consensus transcripts across the pool of the following evidence based tracks: RefSeq, Known Gene, Ensembl, Gencode, AceView, ECgene and ExonWalk, as in Figure 3a. Coded information has been added in front of the track name: asterisks distinguish standard gene tracks, available genome-wide, from an ENCODE only track; a U track predicts a unique model per gene; P predicts protein coding regions only.

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