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Table 3 Exon prediction accuracy using different ExAlt parameter settings.

From: A phylogenetic generalized hidden Markov model for predicting alternatively spliced 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
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
  1. 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.