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 4 Comparison of specificity, sensitivity and F1 scores of transcripts assemblies generated by Strawberry, Scallop, Stringtie, PsiCLASS and FINDER for three model organisms—A. thaliana, O. sativa and Z. 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 (RefSeq)
	STRAWBERRY	SCALLOP	STRINGTIE	PSICLASS	FINDER	STRAWBERRY	SCALLOP	STRINGTIE	PSICLASS	FINDER	STRAWBERRY	SCALLOP	STRINGTIE	PSICLASS	FINDER
Base specificity	38.41	37.34	58.35	62.63	74.46	22.6	24.23	39.83	36.64	42.46	30.06	29.6	49.33	55.61	62.97
Base sensitivity	87.06	85.3	80.22	70.83	71.45	78.2	77.64	70.87	60.27	61.43	81.2	79.08	76.98	70.52	72.1
Base F1 score	53.3	51.94	67.56	66.48	72.92	35.07	36.93	51	45.57	50.21	43.88	43.08	60.13	62.18	67.23
Exon specificity	43.86	70.64	74.82	89.82	91.79	23.51	42.97	51.7	66.29	67.67	37.18	52.37	60.33	77.76	79.71
Exon sensitivity	85.3	79.67	79.29	69.54	69.93	79.08	76.65	75.47	65.75	64.81	85.03	81.68	81.77	75.88	74.38
Exon F1 score	57.93	74.88	76.99	78.39	79.38	36.24	55.07	61.36	66.02	66.21	51.74	63.82	69.43	76.81	76.95
Intron specificity	55.32	78.7	80.58	95.29	96.55	29.13	48.56	56.5	71.41	73.24	43.79	56.74	64.79	82.8	84.86
Intron sensitivity	92.06	89.99	87.75	77.63	76.51	85.84	85.41	83.28	71.72	71.03	90.19	86.69	86.05	78.99	78.12
Intron F1 score	69.11	83.97	84.01	85.56	85.37	43.5	61.92	67.32	71.56	72.12	58.96	68.59	73.92	80.85	81.35
Transcript specificity	6.88	24.84	35.02	56.82	60.04	1.59	9.03	14.26	24.22	24.54	6.96	17.8	26.23	43.96	44.78
Transcript sensitivity	31.68	32.19	35.23	31.8	37.21	26.69	29.43	31.2	32.37	33	48.71	46.71	47.76	42.48	42.25
Transcript F1 score	11.3	28.04	35.12	40.78	45.95	3	13.82	19.57	27.71	28.15	12.18	25.78	33.86	43.21	43.48
Gene specificity	33.16	36.51	63.7	65.67	67.33	17.61	20.16	35.69	40.39	32.79	21.83	26.33	47.43	54.04	52.3
Gene sensitivity	44.77	46.18	50.59	49.33	57.96	28.91	31.79	33.65	34.54	35.05	55.2	55.85	58.03	57.22	57.35
Gene F1 score	38.1	40.78	56.39	56.34	62.29	21.89	24.67	34.64	37.24	33.88	31.29	35.79	52.2	55.58	54.71

Best performance is indicated by bold values

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com

BMC Bioinformatics

Contact us