A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons

Table 3 Exon prediction accuracy using different ExAlt parameter settings.

	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
Ex Alt-Exon- ab initio	100	88	100	85	69	83	70	87	87	84
ExAlt-Frame	96	95	70	80	53	87	48	82	72	89
Ex Alt- Frame- ab initio	97	87	72	74	56	76	48	80	74	82
ExAlt-Frame-Single	96	97	69	85	45	92	31	92	66	94
ExAlt-Default	89	84	58	63	49	77	43	74	67	79
Ex Alt-Default-ab initio	89	75	58	55	50	67	36	58	65	69
ExAlt-Default-Single	89	90	56	66	41	84	28	83	61	85
N-SCAN	87	84	51	80	33	66	31	66	57	78
Augustus	75	77	27	53	27	59	26	57	47	69
SNAP	76	72	42	61	29	56	27	62	50	67

Columns are organized by exon type: Constitutive, Cassette, Multiple Splice, Intron Retention, and all exons counted together (All Exons). Rows 1–2 show ExAlt performance using an input exon and default parameters from Table 2 (ExAlt-Exon) and no informant species (ExAlt-Exon-ab initio). Rows 3–5 show ExAlt performance using an input coding frame with default parameters (ExAlt-Frame), no informant species (ExAlt-Frame-ab initio), and at most 1 exon predicted per test sequence (ExAlt-Frame-Single). Rows 6–8 show ExAlt performance using no gene structure information with default parameters (ExAlt-Default), no informant species (ExAlt-Default-ab initio), and at most 1 exon prediction per test sequence (ExAlt-Default-Single). Output is shown for three single isoform gene finders N-SCAN, Augustus, and SNAP.

ISSN: 1748-7188