Analysing RNA-kinetics based on folding space abstraction

Huang, Jiabin; Voß, Björn

doi:10.1186/1471-2105-15-60

BMC Bioinformatics

Table 1 Fractions of locally optimal hishreps

From: Analysing RNA-kinetics based on folding space abstraction

Instance	Length	π _a	π _m	π _h+	π _h	$π_{a}^{SN}$	$π_{m}^{SN}$	$π_{h +}^{SN}$	$π_{h}^{SN}$
		[%]
SL	56 nt	79.00	98.00	98.00	99.00	73.00	85.00	94.29	96.88
		90.80	24.32	21.17	18.37	56.59	2.63	2.56	2.40
attenuator	73 nt	81.00	100.00	100.00	100.00	77.00	99.00	96.00	92.00
		94.19	32.15	23.98	18.90	76.24	14.41	2.38	0.95
ms2	73 nt	84.00	98.00	98.00	97.00	82.00	89.00	80.00	81.00
		91.30	15.96	11.84	10.85	79.61	1.31	0.38	0.29
s15	74 nt	87.00	100.00	100.00	100.00	82.00	96.00	97.00	100.00
		90.63	16.45	13.30	10.96	73.21	4.23	1.28	0.85
dsrA	85 nt	77.00	98.00	98.00	99.00	71.00	97.00	98.00	100.00
		83.70	27.30	22.58	16.39	57.26	4.56	2.00	0.76
rb2	113 nt	76.00	92.00	92.00	93.00	75.00	88.00	88.00	85.00
		79.17	28.13	27.38	22.79	74.26	12.92	11.50	7.10
alpha operon	130 nt	99.00	98.00	96.00	96.00	98.00	100.00	99.00	100.00
		96.12	9.82	4.15	2.22	72.59	1.26	0.45	0.28
rb3	141 nt	76.00	99.00	99.00	99.00	76.00	99.00	99.00	98.00
		96.20	30.56	21.48	17.52	96.20	23.24	10.61	8.11
amv	145 nt	77.00	89.00	89.00	83.00	78.00	89.00	89.00	81.00
		82.80	38.03	38.03	4.56	83.87	38.03	38.03	4.45
rb4	146 nt	96.00	100.00	100.00	100.00	97.00	100.00	99.00	81.00
		89.72	10.80	8.04	5.03	20.51	2.35	1.36	0.88
rb1	148 nt	86.00	100.00	100.00	100.00	81.00	100.00	99.00	98.00
		72.27	8.87	6.61	5.67	61.36	4.84	1.66	1.21
HDV	153 nt	96.00	100.00	100.00	100.00	96.00	100.00	99.00	98.00
		87.27	37.04	5.62	2.64	87.27	26.74	2.61	1.00
thiM leader	165 nt	85.00	100.00	100.00	100.00	82.00	100.00	100.00	100.00
		98.84	24.33	15.72	9.00	86.32	18.38	7.94	5.01
rb5	201 nt	100.00	100.00	99.00	99.00	100.00	100.00	99.00	97.00
		93.46	29.07	4.06	2.24	93.46	25.06	2.24	0.78
sbox leader	247 nt	77.00	76.00	68.00	60.00	68.00	65.00	42.00	15.00
		91.67	28.36	15.70	6.76	58.62	14.84	3.11	0.42
HIV-1 leader	280 nt	39.00	71.00	58.00	56.00	38.00	52.00	38.00	38.00
		48.75	2.09	1.34	1.21	47.50	1.20	0.60	0.54
ribD leader	304 nt	91.00	100.00	85.00	85.00	88.00	92.00	76.00	70.00
		81.25	37.17	8.83	5.53	78.57	29.21	6.23	3.18
hok	396 nt	58.00	79.00	69.00	62.00	57.00	83.00	72.00	65.00
		53.70	1.42	0.70	0.51	52.78	1.38	0.60	0.42

In each cell, the upper number represents the fraction of the set of hishreps that are also locally optimal $(\frac{| ℋ \cap ℒ |}{| ℋ |})$ and the lower number represents the fraction of the set of local optima that are also hishreps $(\frac{| ℋ \cap ℒ |}{| ℒ |})$ . We restricted the computation of hishapes to the best 100 and the computation of the local optima to the corresponding energy range $max {Δ G (x) : x \in ℋ}$ above the MFE. The dataset is taken from [12]. ^SN strictly negative hishapes.

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