Swellix: a computational tool to explore RNA conformational space

BMC Bioinformatics

Table 4 Comparison of Serial and Parallel Runtimes for Longer RNA Sequences

Sequence	Minimum Helix Length	Bundled Structures	Parallel Runtime (s)	Serial Runtime (s)
tRNA-1EHZ	2	1,327,023,534	456.28	11,117.55
tRNA-1EHZ	3	563,026	3.25	7.61
tRNA-1EHZ	4	8292	4.71	10.24
tRNA-1EHZ	5	314	45.32	137.53
tRNA-1EHZ	6	33	718.27	2498.52
HERV 141	3	12,518,055,094	5550.62	112,162.24
HERV 141	4	1,463,580	8.06	22.24
HERV 141	5	3401	41.97	130.4
HERV 141	6	43	663.51	2303.08
HERV 244	5	195,971,275	256.02	2229
HERV 244	6	59,909	2116.68	7239.21
HERV 418	6	7,514,046,365	10,040.77	97,296.14

Swellix computations were run with the parallelized bundling option on the Blue Waters computer. Each sequence was given the same number of cores as nucleotides in the sequence, ie tRNA-1EHZ has 76 nucleotides and cores. There are three HERV RNA sequences of different lengths: 141, 244, and 418 nucleotides [46]. HERV141 is the shortest known HERV RNA fragment, and HERV418 is a self-folding domain that binds the Rev. protein [47]

ISSN: 1471-2105