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Furthermore, a parallel version of the HelixPSO is proposed.<\/jats:p><\/jats:sec><jats:sec><jats:title content-type=\"abstract-heading\">Findings<\/jats:title><jats:p>For a set of standard RNA test sequences it is shown experimentally that HelixPSO obtains a better average sensitivity than SARNA\u2010Predict and SetPSO and is as good as RNA\u2010Predict and RNAfold. When best values for different measures (e.g. number of correctly predicted base pairs, false positives and sensitivity) over several runs are compared, HelixPSO performs better than RNAfold, similar to RNA\u2010Predict, and is outperformed by SARNA\u2010Predict. It is shown that HelixPSO complements RNA\u2010Predict and SARNA\u2010Predict well since the algorithms show often very different behavior on the same sequence. For the parallel version of HelixPSO it is shown that good speedup values can be obtained for small to medium size PC clusters.<\/jats:p><\/jats:sec><jats:sec><jats:title content-type=\"abstract-heading\">Originality\/value<\/jats:title><jats:p>The new PSO algorithm HelixPSO for finding RNA secondary structures uses different algorithmic ideas than the other existing PSO algorithm SetPSO. HelixPSO uses thermodynamic information as well as the centroid as a reference structure and is based on a multiple swarm approach.<\/jats:p><\/jats:sec>","DOI":"10.1108\/17563781111136685","type":"journal-article","created":{"date-parts":[[2011,6,18]],"date-time":"2011-06-18T07:18:29Z","timestamp":1308381509000},"page":"160-186","source":"Crossref","is-referenced-by-count":9,"title":["Particle swarm optimization for finding RNA secondary structures"],"prefix":"10.1108","volume":"4","author":[{"given":"Michael","family":"Geis","sequence":"first","affiliation":[]},{"given":"Martin","family":"Middendorf","sequence":"additional","affiliation":[]}],"member":"140","reference":[{"key":"key2022032020101193500_b1","doi-asserted-by":"crossref","unstructured":"Alba, E. (2005), Parallel Metaheuristics: A New Class of Algorithms, Wiley, New York, NY.","DOI":"10.1002\/0471739383"},{"key":"key2022032020101193500_b3","doi-asserted-by":"crossref","unstructured":"Benedetti, G. and Morosetti, S. (1995), \u201cA genetic algorithm to search for optimal and suboptimal RNA secondary structures\u201d, Biophysical Chemistry, Vol. 55, pp. 253\u20109.","DOI":"10.1016\/0301-4622(94)00130-C"},{"key":"key2022032020101193500_b4","doi-asserted-by":"crossref","unstructured":"Birattari, M. and Dorigo, M. (2007), \u201cHow to assess and report the performance of a stochastic algorithm on a benchmark problem: mean or best result on a number of runs?\u201d, Optimization Letters, Vol. 1, pp. 309\u201011.","DOI":"10.1007\/s11590-006-0011-8"},{"key":"key2022032020101193500_b5","unstructured":"Burns, G., Daoud, R. and Vaigl, J. (1994), \u201cLAM: an open cluster environment for MPI\u201d, in Ross, J.W. (Ed.), Proceedings of Supercomputing Symposium, Columbus, OH, pp. 379\u201086."},{"key":"key2022032020101193500_b6","doi-asserted-by":"crossref","unstructured":"Cannone, J.J., Subramanian, S., Schnare, M.N., Collett, J.R., D'Souza, L.M., Du, Y., Feng, B., Lin, N., Madabusi, L.V., M\u00fcller, K.M., Pande, N., Shang, Z., Yu, N. and Gutell, R.R. (2002), \u201cThe comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal intron, and other RNAs\u201d, BMC Bioinformatics, Vol. 3, p. 15.","DOI":"10.1186\/1471-2105-3-15"},{"key":"key2022032020101193500_b7","doi-asserted-by":"crossref","unstructured":"Chen, J.H., Le, S.Y. and Maizel, J.V. (2000), \u201cPrediction of common secondary structures of RNAs: a genetic algorithm approach\u201d, Nucleic Acids Research, Vol. 28, pp. 991\u20109.","DOI":"10.1093\/nar\/28.4.991"},{"key":"key2022032020101193500_b8","doi-asserted-by":"crossref","unstructured":"de Smit, M. and van Duin, J. (1990), \u201cControl of prokaryotic translation initiation by mRNA secondary structure\u201d, Progress in Nucleic Acid Research in Molecular Biology, Vol. 38, pp. 1\u201035.","DOI":"10.1016\/S0079-6603(08)60707-2"},{"key":"key2022032020101193500_b9","doi-asserted-by":"crossref","unstructured":"Doudna, J.A. (2000), \u201cStructural genomics of RNA\u201d, Nature Structural Biology, Vol. 7, pp. 954\u20106.","DOI":"10.1038\/80729"},{"key":"key2022032020101193500_b10","unstructured":"Engelbrecht, A.P. (2006), Fundamentals of Computational Swarm Intelligence, Wiley, New York, NY."},{"key":"key2022032020101193500_b11","doi-asserted-by":"crossref","unstructured":"Geis, M. and Middendorf, M. (2007), \u201cA particle swarm optimizer for finding minimum free energy RNA secondary structures\u201d, Proceedings of IEEE Swarm Intelligence Symposium, pp. 461\u20108.","DOI":"10.1109\/SIS.2007.368019"},{"key":"key2022032020101193500_b13","unstructured":"Goldberg, D.E. and Lingle, R.J. 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