Table 3. Performance of programs on the ENCODE IMR90 data: features (full-transcripts and introns) matching known and/or high-confidence novel annotations. GENCODE v.17 chromosome 1 annotation contains 15 493 transcripts and 33 202 introns. R = (recall) = Match/Annotations, P = (precision) = Match/Predicted.

Program	Transcripts				Introns
	Predicted	Match	R	P	Predicted	Match	R	P
Cytosol
CLASS2	3029	1053	0.068	0.348	12 662	12 557 (11 996)	0.378 (0.361)	0.968 (0.947)
CLASS2_F0.01	3836	1183	0.076	0.308	13 413	13 253 (12 327)	0.399 (0.371)	0.988 (0.919)
Cufflinks	2508	621	0.040	0.248	10 420	10 372 (10 109)	0.312 (0.304)	0.995 (0.970)
Cufflinks_F0.01	3458	719	0.046	0.208	11 725	11 564 (10 779)	0.348 (0.325)	0.986 (0.919)
IsoCEM	2479	722	0.047	0.291	11 483	11 297 (10 617)	0.340 (0.320)	0.984 (0.925)
Scripture	14 621	971	0.063	0.066	13 820	12 751 (11 149)	0.384 (0.336)	0.923 (0.807)
iReckon	4512	1730	0.112	0.383	11 724	11 477 (10 552)	0.346 (0.318)	0.979 (0.900)
Nucleus
CLASS2	6084	992	0.064	0.163	16 391	15 765 (12 862)	0.475 (0.418)	0.962 (0.846)
CLASS2_F0.01	10 216	1141	0.074	0.112	18 610	17 699 (14 539)	0.532 (0.438)	0.950 (0.781)
Cufflinks	2714	561	0.036	0.207	11 255	11 079 (10 576)	0.334 (0.319)	0.984 (0.940)
Cufflinks_F0.01	6085	789	0.051	0.130	16 884	16 064 (13 568)	0.484 (0.409)	0.951 (0.804)
IsoCEM	2236	277	0.018	0.124	9604	8737 (7576)	0.263 (0.228)	0.910 (0.789)
Scripture	45 247	764	0.049	0.017	18 048	13 910 (10 188)	0.419 (0.307)	0.771 (0.564)
iReckon	5769	1539	0.099	0.267	10 162	9474 (8232)	0.285 (0.248)	0.932 (0.810)