Table 2.

Assessment of the Annotation Set

	Total annotation set				Coding genes only				ORF of coding genes				Pseudogenes
	Sn	Sp	G	E	Sn	Sp	G	E	Sn	Sp	G	E	Sn	Sp	G	E
cDNA
dbEST	0.77	0.42	0.97	0.92	0.80	0.32	0.98	0.92	0.85	0.17	0.98	0.93	0.71	0.08	0.97	0.93
EMBL_vertrna	0.69	0.79	0.88	0.87	0.74	0.62	0.88	0.87	0.87	0.36	0.92	0.91	0.62	0.14	0.92	0.87
Human	0.68	0.79	0.82	0.83
Mouse	0.10	0.96	0.49	0.28
Other	0.11	0.93	0.38	0.24
Protein databases	0.55	0.31	0.91	0.89	0.58	0.24	0.93	0.90	0.94	0.19	0.98	0.94	0.55	0.06	0.91	0.87
Comparative
Mus blat	0.29	0.66	0.77	0.59	0.33	0.55	0.81	0.60	0.60	0.49	0.88	0.64	0.24	0.11	0.73	0.59
Mus exo	0.26	0.57	0.79	0.54	0.28	0.45	0.80	0.53	0.49	0.40	0.88	0.56	0.25	0.11	0.79	0.60
Exofish	0.13	0.92	0.59	0.38	0.15	0.76	0.64	0.38	0.29	0.75	0.72	0.42	0.12	0.16	0.54	0.45
Prediction
Genscan	0.39	0.68	0.79	0.79	0.46	0.59	0.90	0.82	0.88	0.56	0.95	0.87	0.24	0.08	0.61	0.57
fgenesh	0.35	0.76	0.70	0.75	0.42	0.67	0.82	0.79	0.82	0.63	0.89	0.85	0.19	0.08	0.48	0.51
Multiple
GS+blata	0.27	0.95	0.62	0.49	0.32	0.85	0.75	0.52	0.65	0.83	0.85	0.58	0.13	0.09	0.38	0.30
Fish + mouseb	0.11	0.95	0.54	0.31	0.12	0.79	0.59	0.31	0.25	0.78	0.67	0.34	0.09	0.16	0.47	0.35

Note that for the subdivided data, the specificity calculation includes all matches and so will be reduced relative to the total annotation. Comparisons of specificity are therefore only fair within columns.

^aGenScan exons aligned with a blat mouse match.

^bExofish matches that align with a mouse match from either method.

(Sn) Sensitivity (including all immunoglobulin λ [IGL] segments); (Sp) specificity (including all IGL segments); (G) gene hits (only counting [GLC] segments); (E) exon hits (only counting immunoglobulin λ constant [IGLC] segments).