PHDcleav: a SVM based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors

Table 3 Performance of 'quikfold' derived sequence- and structure-based SVM models for Dicer cleavage sites at 5p arm.

Features	Window size	CD-5p (sequence-based)				CD-5p (structure-based)
		Sn	Sp	Ac	Mc	Sn	Sp	Ac	Mc
Mono	8	56.76	56.94	56.85	0.14	69.37	70.45	69.91	0.40
	10	59.10	56.40	57.75	0.16	75.68	77.48	76.58	0.53
	12	54.05	57.84	55.95	0.12	77.84	83.06	80.45	0.61
	14	58.20	59.64	58.92	0.18	81.44	82.70	82.07	0.64
Dinuc	8	58.92	59.46	59.19	0.18	65.95	67.03	66.49	0.33
	10	55.50	61.08	58.29	0.17	67.39	67.57	67.48	0.35
	12	59.82	56.76	58.29	0.17	69.73	74.41	72.07	0.44
	14	64.14	54.95	59.55	0.19	73.33	73.33	73.33	0.47
Trinuc	8	61.98	52.43	57.21	0.14	60.36	59.10	59.73	0.19
	10	55.32	50.45	52.88	0.06	66.31	62.34	64.32	0.29
	12	57.48	56.58	57.03	0.14	65.77	65.41	65.59	0.31
	14	61.26	60.18	60.72	0.21	68.65	65.41	67.03	0.34
Binary	8	62.70	58.92	60.81	0.22	69.55	78.02	73.78	0.48
	10	61.26	59.46	60.36	0.21	76.40	80.36	78.38	0.57
	12	65.41	63.42	64.41	0.29	82.16	81.26	81.71	0.63
	14	62.52	69.73	66.13	0.32	85.23	87.21	86.22	0.72

Models were developed using composition and binary pattern of different window sizes. Patterns were taken from sequence of Dicer cleavage site of 5p arm (sequence of CP-5p) and structure of Dicer cleavage site of 5p arm (structure of CP-5p).

ISSN: 1471-2105