Swellix: a computational tool to explore RNA conformational space

BMC Bioinformatics

Table 1 Swellix Run Times for RNA Sequences

Sequence	Nucleotides	Components	Components w/ bundling	Bundles	Structures	w/ bundling	Runtime (s)	Runtime (s) w/ bundling	Bundling Time Efficiency (%)
14mer	14	12	8	8	15	8	0.2	0.29
28mer	28	53	40	28	833	374	0.2	0.4
42mer	42	130	108	48	67,014	25,862	0.35	0.58
MicA	50	221	193	71	1,127,719	391,111	3.27	1.7	48.0
tRNA asp 7	71	578	526	141	14,676,607,199	3,586,825,719	51,708.28	12,627.35	75.6
tRNA RG1660	74	471	436	98	2,098,681,265	658,285,383	7140.63	2216.78	69.0
tRNA 1EHZ	76	533	495	107	3,820,164,477	1,327,023,534	13,577.62	4685.58	65.5

Swellix computations were run with and without the bundling option on the Schooner computer and a minimum helix length of 2. The reduction in the number of components, the number of structures, and the runtimes with the bundling option are highlighted in blue. Bundling time efficiency is calculated as the difference in runtimes with and without bundling divided by the runtime without bundling. For the very short sequences with less than 1 s runtime, the time to perform the bundling step increases the overall runtime. The 14mer sequence is 5′5’GCUCUAAAAGAGAG 3′. The 28mer and 42mer are concatamers of the 14mer sequence. The MicA sequence is a domain of a bacterial noncoding RNA [40]. The three tRNA sequences are tRNA Asp 7 from Homo sapiens [41], tRNA Ala from Shigella sonnei [42], and tRNA Phe from Sacchromyces cerevisiae (PDB# 1EHZ) [43]

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