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. 2018 Nov;24(11):1555–1567. doi: 10.1261/rna.066324.118

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© 2018 Bellaousov et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society

This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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FIGURE 3. — Time performance for long sequences. Designs were made for sequences of up to 1995 nt (Supplemental Table S7). Mean time performance is shown for ten calculations for each target structure. Design times were capped at 75 d of running time (6,480,000 sec). Points missing for NUPACK (697, 1793, and 1995 nt) and Design_Random (1793 and 1995 nt) had one or more designs that reached the maximum runtime and were terminated, so the mean could not be calculated. Design_Random and Design_Preselected were run with default parameters. NUPACK was run using rna99 thermodynamic parameters at 37°C, the NED threshold was set to 0.1 so that NUPACK produced structures of similar NED as Design_Random, and other parameters were set to defaults. Designs were performed on a single core of an Opteron 2427 processor.