NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome

Table 1

Sensitivity of NOVOMIR, TRIPLET-SVM [14], and HHMMIR [13] in pre-miRNA prediction for different versions of MIRBASE. The row “14–10” shows values for sequences from MIRBASE 14 which are not present in MIRBASE 10.

			Sensitivity1
MIRBASE			NOVOMIR2		HHMMIR3		TRIPLET-SVM3
version	# sequences		pre-miRNA	miRNA/miRNA*	pre-miRNA		pre-miRNA
10	184	A. th.	0.84	0.73	0.15	0.75	0.45	0.60
14	190	A. th.	0.83	0.75	0.10	0.79	0.44	0.59
10	1247	plant	0.79	0.82	0.04	0.58	0.39	0.51
14	2030	plant	0.79	0.83	0.04	0.64	0.38	0.50
14–10	788	plant	0.80	—	0.04	0.73	0.38	0.48

1 Sensitivity is calculated as 𝑇𝑃/(𝑇𝑃+𝐹𝑁).
2 Note that NOVOMIR’s thresholds and probabilities were learned only from A. thaliana sequences in MIRBASE version 10.
3 The left column gives sensitivity for all sequences; the right column gives sensitivity for those sequences left after the preprocessing step(s) of HHMMIR and TRIPLET-SVM, respectively.