A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons

Table 2 Prediction performance of ExAlt. Sensitivity (Sens) and Specificity (Spec) are shown for exons.

	Constitutive		Cassete		Multiple Splice		Intron Retention		All Exons
	Sens	Spec	Sens	Spec	Sens	Spec	Sens	Spec	Sens	Spec
ExAlt-Exon	100	96	100	89	67	94	61	89	84	94
N-SCAN-Exon Union	100	86	100	89	65	79	55	78	82	84
Augustus-Exon Union	100	82	100	81	63	77	52	73	81	79
SNAP-Exon Union	100	77	100	79	64	74	51	76	81	77
SNAP+N-SCAN-Exon Union	100	73	100	74	69	68	57	70	83	72
Augustus+N-SCAN-Exon Union	100	79	100	77	68	73	57	68	83	76
Aug.+SNAP+N-SCAN-Exon Union	100	70	100	69	71	64	60	64	84	67

Columns are organized by exon type: Constitutive, Cassette, Multiple Splice, Intron Retention, and all exons counted together (All Exons). Row 1 shows ExAlt performance using an input exon and default parameter settings (ExAlt-Exon). Rows 2–6 show the union of different combinations of three gene finders (N-SCAN, SNAP, and Augustus) plus the input exon. (Aug. = Augustus)

ISSN: 1748-7188