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

BMC Bioinformatics

Table 3 Comparison of RNAspa's run-time with that of other methods

Family	Average run-time per sequence in seconds
	RNAspa	StemLoc	pmMulti	FoldAlignM	RNAcast
tRNA	13	47	21	549	<1
Tymo	8	70	12	93	<1
SAM	13	3	18	248	<1
Lysine	20	11	69	1076	<1
Purine	84	339	135	1518	<1
Cobalamin	133	105	no data	no data	<1
FMN	56	6	141	5042	<1
glmS	58	60	no data	no data	no data

For all datasets, except glmS which did not yield results, the runtime of RNAcast was less than one second. RNAspa always ran faster than pmMulti and FoldAlignM. In four of eight families it ran faster than StemLoc and its overall running time is better than StemLoc's run-time.

ISSN: 1471-2105