Table 2.

Accuracy values of variants of AUGUSTUS on the ENCODE test set with 296 genes and an average of 2.2 transcripts per gene

	Single transcript	Few transcripts	Medium number of transcripts	Many transcripts
Gene sensitivity	0.233	0.273	0.294	0.345
Gene specificity	0.170	0.200	0.211	0.239
Transcript sensitivity	0.106	0.125	0.137	0.165
Transcript specificity	0.170	0.144	0.112	0.053
Exon sensitivity	0.527	0.540	0.557	0.600
Exon specificity	0.639	0.615	0.571	0.490
Base sensitivity	0.775	0.779	0.790	0.814
Base specificity	0.764	0.757	0.738	0.705
Average transcripts/gene	1.0	1.4	2.0	5.1

We used AUGUSTUS with the original single-transcript option and with the new options for ‘few transcripts’, ‘medium number of transcripts’ and ‘many transcripts’.