FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences

Banerjee, Sagnik; Bhandary, Priyanka; Woodhouse, Margaret; Sen, Taner Z.; Wise, Roger P.; Andorf, Carson M.

doi:10.1186/s12859-021-04120-9

Table 1 Sensitivity, Specificity and F1 scores of transcripts generated by multiple gene annotation pipelines for three model organisms—Arabidopsis thaliana, Oryza sativa and Zea mays

From: FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences

	Arabidopsis thaliana						Oryza sativa						Zea mays (NCBI)
	BRAKER2	MAKER2	PASA	FINDER	FINDER + BRAKER2	FINDER + BRAKER2 + PROTEIN	BRAKER2	MAKER2	PASA	FINDER	FINDER + BRAKER2	FINDER + BRAKER2 + PROTEIN	BRAKER2	MAKER2	PASA	FINDER	FINDER + BRAKER2	FINDER + BRAKER2 + PROTEIN
Base specificity	91.08	74.87	62.71	74.46	75.01	75.04	57.63	52.67	36.77	42.46	42.6	42.75	6.52	45.22	60.39	62.97	62.96	62.92
Base sensitivity	60.27	52.55	69.41	71.45	74.14	74.23	36.85	40.17	59.19	61.43	61.83	62.37	50.43	54.38	66.7	72.1	72.15	72.16
Base F1 score	72.54	61.76	65.89	72.92	74.57	74.63	44.95	45.58	45.36	50.21	50.44	50.73	11.55	49.38	63.39	67.23	67.24	67.22
Exon specificity	80.28	95.35	90.74	91.79	91.43	91.43	38.4	72.31	67.37	67.67	67.5	67.62	15.96	65.14	84.26	79.71	79.59	79.57
Exon sensitivity	73.29	55.04	67.49	69.93	71.62	71.7	53.74	50.59	63.99	64.81	65.22	66.06	65.65	61.84	71.84	74.38	74.4	74.4
Exon F1 score	76.63	69.79	77.41	79.38	80.32	80.37	44.79	59.53	65.64	66.21	66.34	66.83	25.68	63.45	77.56	76.95	76.91	76.9
Intron specificity	86	98.26	95.98	96.55	96.26	96.26	52.8	76.87	72.36	73.24	73.19	73.26	21.77	74.41	88.45	84.86	84.78	84.76
Intron sensitivity	84.25	60.64	76.11	76.51	78.33	78.42	76.78	55.77	70.44	71.03	71.52	72.34	80.88	64.99	75.19	78.12	78.15	78.15
Intron F1 score	85.12	75	84.9	85.37	86.37	86.43	62.57	64.64	71.39	72.12	72.35	72.8	34.31	69.38	81.28	81.35	81.33	81.32
Transcript specificity	49.91	76.9	55.21	60.04	59.82	59.82	12.71	40.13	23.17	24.54	24.59	24.54	2.75	32.67	48.6	44.78	44.84	44.78
Transcript sensitivity	30.26	21.74	28.62	37.21	39.21	39.28	16.35	18.01	29.51	33	33.32	33.82	19.57	25.01	37.94	42.25	42.3	42.31
Transcript F1 score	37.68	33.9	37.7	45.95	47.37	47.42	14.3	24.86	25.96	28.15	28.3	28.44	4.82	28.33	42.61	43.48	43.53	43.51
Gene specificity	51.58	76.9	61.79	67.33	66.56	66.55	13.46	40.13	36.81	32.79	32.76	32.38	2.78	32.67	55.69	52.3	52.29	52.19
Gene sensitivity	50.43	37.2	44.39	57.96	61.3	61.4	18.07	19.4	31.37	35.05	35.4	35.96	29.02	38.14	51.57	57.35	57.42	57.43
Gene F1 score	51	50.14	51.66	62.29	63.82	63.87	15.43	26.16	33.87	33.88	34.03	34.08	5.07	35.19	53.55	54.71	54.74	54.68

Best performance is indicated by bold values

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