%0 Journal Article %1 Tsang_2015_IJICC %A Tsang, Herbert H. %A Wiese, Kay C. %D 2015 %J International Journal of Intelligent Computing and Cybernetics %K imported tsang_pub %N 2 %P 152-171 %R 10.1108/IJICC-02-2015-0007 %T A study of different annealing schedules in SARNA-predict: A permutation based SA algorithm for RNA folding %U /brokenurl# http://dx.doi.org/10.1108/IJICC-02-2015-0007 %V 8 %X Purpose – The purpose of this paper is to present a study of the effect of different types of annealing schedules for a ribonucleic acid (RNA) secondary structure prediction algorithm based on simulated annealing (SA). Design/methodology/approach – An RNA folding algorithm was implemented that assembles the final structure from potential substructures (helixes). Structures are encoded as a permutation of helixes. An SA searches this space of permutations. Parameters and annealing schedules were studied and fine-tuned to optimize algorithm performance. Findings – In comparing with mfold, the SA algorithm shows comparable results (in terms of F-measure) even with a less sophisticated thermodynamic model. In terms of average specificity, the SA algorithm has provided surpassing results. Research limitations/implications – Most of the underlying thermodynamic models are too simplistic and incomplete to accurately model the free energy for larger structures. This is the largest limitation of free energy-based RNA folding algorithms in general. Practical implications – The algorithm offers a different approach that can be used in practice to fold RNA sequences quickly. Originality/value – The algorithm is one of only two SA-based RNA folding algorithms. The authors use a very different encoding, based on permutation of candidate helixes. The in depth study of annealing schedules and other parameters makes the algorithm a strong contender. Another benefit is that new thermodynamic models can be incorporated with relative ease (which is not the case for algorithms based on dynamic programming).

@article{Tsang_2015_IJICC, abstract = { Purpose – The purpose of this paper is to present a study of the effect of different types of annealing schedules for a ribonucleic acid (RNA) secondary structure prediction algorithm based on simulated annealing (SA). Design/methodology/approach – An RNA folding algorithm was implemented that assembles the final structure from potential substructures (helixes). Structures are encoded as a permutation of helixes. An SA searches this space of permutations. Parameters and annealing schedules were studied and fine-tuned to optimize algorithm performance. Findings – In comparing with mfold, the SA algorithm shows comparable results (in terms of F-measure) even with a less sophisticated thermodynamic model. In terms of average specificity, the SA algorithm has provided surpassing results. Research limitations/implications – Most of the underlying thermodynamic models are too simplistic and incomplete to accurately model the free energy for larger structures. This is the largest limitation of free energy-based RNA folding algorithms in general. Practical implications – The algorithm offers a different approach that can be used in practice to fold RNA sequences quickly. Originality/value – The algorithm is one of only two SA-based RNA folding algorithms. The authors use a very different encoding, based on permutation of candidate helixes. The in depth study of annealing schedules and other parameters makes the algorithm a strong contender. Another benefit is that new thermodynamic models can be incorporated with relative ease (which is not the case for algorithms based on dynamic programming). }, added-at = {2021-09-21T08:20:54.000+0200}, author = {Tsang, Herbert H. and Wiese, Kay C.}, biburl = {https://www.bibsonomy.org/bibtex/237416d9f339e022dba95d51697f687dc/herberttsang}, doi = {10.1108/IJICC-02-2015-0007}, eprint = {http://dx.doi.org/10.1108/IJICC-02-2015-0007}, interhash = {6d2a15697e75fb90f0e82a62ad6bb6ae}, intrahash = {37416d9f339e022dba95d51697f687dc}, journal = {International Journal of Intelligent Computing and Cybernetics}, keywords = {imported tsang_pub}, number = 2, pages = {152-171}, timestamp = {2021-09-21T08:22:40.000+0200}, title = {A study of different annealing schedules in SARNA-predict: A permutation based SA algorithm for RNA folding}, url = {/brokenurl# http://dx.doi.org/10.1108/IJICC-02-2015-0007 }, volume = 8, year = 2015 }