Analysing RNA-kinetics based on folding space abstraction

BMC Bioinformatics

Table 2 Comparison of BARRIERS (BAR), BFS , RNATABUPATH ( TABU ), RNAEAPATH (EA) and HIPATH

Instance	Length	BAR	BFS	TABU	EA	HIPATH	HIPATH2
			(k = 10)	(n = 1000)
rb1	148 nt	-	24.04	24.04	23.2	20.94	20.94
rb2	113 nt	*	8.2	7.25	6.5	6.6	6.6
rb3	141 nt	-	22.4	17.9	17.5	16.7	16.7
rb4	146 nt	-	16.9	16.9	16.9	16.9	16.9
rb5	201 nt	-	24.54	24.54	21.44	21.44	21.44
hok	396 nt	-	28.5	29.66	20.7	21.1	21.1
SL	56 nt	11.8	13	12.9	13	12.4	12.4
attenuator	73 nt	8.3	8.7	8.6	8.7	8.6	8.5
s15	74 nt	6.6	7.1	6.6	7.1	7.1	6.6
sbox leader	247 nt	*	5.2	5.2	5.2	5.2	5.2
thiM leader	165 nt	-	16.13	14.84	12.3	14	12.4
ms2	73 nt	*	6.6	6.6	6.6	6.6	6.6
HDV	153 nt	-	17.4	17	16.8	15.6	15.6
dsrA	85 nt	8	8.3	8.2	8	8.3	8
ribD leader	304 nt	-	10.71	9.5	9.5	10.71	9.5
amv	145 nt	*	5.8	5.8	5.74	5.8	5.5
alpha operon	130 nt	*	6.5	6.5	6.1	6.5	5.96
HIV-1 leader	280 nt	-	9.3	11.3	8.9	9.3	9.3

The dataset was taken from [12, 19], the results for BFS and RNATABUPATH from [12] and the results for EA from [13]. Energy barriers are given in kcal/mol. The maxkeep value k was 10 for BFS itself and for the BFS used within HIPATH and HIPATH2. HIPATH2 was used with auto-adjusted fuzzy related hishape numbers, π_a and θ=1.5. HIPATH was used with the default parameters. Bold numbers represent the minimum value for the respective sequence. The symbol "*" means BARRIERS could not be applied because either the start or the target structure was not locally optimal. The symbol "-" means computation did not finish within one day. The energy range used with RNASUBOPT for BARRIERS was determined using HIPATH2 and set to the barrier energy of HIPATH2 + 1 kcal/mol. Note that the results may be different from the ones shown in [14] since the used start and target structures may differ. Here we used the ones provided in [12], while in [14] we derived them for ourselves.

ISSN: 1471-2105