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Table 1 Swellix Run Times for RNA Sequences

From: Swellix: a computational tool to explore RNA conformational space

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
  1. 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]