Random versus Deterministic Descent in RNA Energy Landscape Analysis

Table 3

Observed local minima: percentage of observed local minima, , relative to found by each descent procedure for the same set of conformations (i.e., last three columns in %); equals the length of sequences and is the number of local minima identified by RNAsubopt and Barriers within the partial energy landscapes.

Number	Gene				Gradient	Random	First
					lm()	lm()	lm()
1	PAX7	99	50,861	1.0	63.55	72.64	74.53
2	OXT	99	74,426	1.0	61.74	67.41	72.70
3	GMEB1	113	466,093	2.0	54.54	56.54	57.76
4	LIG3	124	317,284	1.0	42.72	45.50	49.12
5	CBR1	284	643,999	1.5	49.40	48.95	52.07
6	HTR3E	302	533,316	1.5	42.42	44.34	43.55
7	HLA-G	386	906,393	2.5	51.49	52.92	52.99
8	ALDH4A1	400	540,609	1.5	51.06	46.94	51.69
9	MRPL9	407	41,979	1.0	60.44	61.08	61.19
10	AQP5	504	714,812	2.0	58.02	57.98	58.72
Average					53.54	55.43	57.43