Markup | Genome Research

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+blat[ii]	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 + mouse[iii]	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

[i] 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.

[ii] GenScan exons aligned with a blat mouse match.

[iii] Exofish matches that align with a mouse match from either method.

[iv] (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).