RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules

BMC Bioinformatics

Table 2 Comparing the performance of RNAspa in 'Complete Enumeration' and 'Boltzmann Sampling' modes

Family	Avg. length and STD	Complete Enumeration		Boltzmann Sampling
		Time	MCC	Time	MCC
tRNA	71 ± 4	6.24	0.86	6.51	0.84
Tymo	79 ± 3	6.22	0.93	7.14	0.92
SAM	111 ± 15	14.7	0.66	14.6	0.72
Lysine	179 ± 7	48.53	0.68	45.7	0.72
Purine	96 ± 1	9.53	0.86	9.47	0.84
Cobalamin	200 ± 27	70.25	0.40	71.12	0.43
FMN	135 ± 19	30.08	0.44	25.73	0.49
glmS	159 ± 40	38.79	0.61	33.62	0.64

The time columns indicate the average run-time in seconds per sequence for the corresponding modes of running RNAsubopt. The 'complete enumeration' mode performed better on shorter sequences (tRNA, Tymo, Purine) and the 'Boltzmann sampling' mode performed better on longer sequences (SAM, Cobalamin, FMN, glmS). See [Additional File 6] for raw data.

ISSN: 1471-2105