An efficient simulated annealing algorithm for the RNA secondary structure prediction with Pseudoknots
| Autor: | Liu Jun, Wang Yuting, Lv Yulin, He Juanjuan, Zhang Kai |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
Pseudoknot
lcsh:QH426-470 Base pair lcsh:Biotechnology 0206 medical engineering 02 engineering and technology Biology Nucleic acid secondary structure 03 medical and health sciences lcsh:TP248.13-248.65 Genetics Base Pairing Rna secondary structure prediction 030304 developmental biology Minimum free energy 0303 health sciences Research Simulated annealing algorithm Data structure RNA secondary structure Random matching lcsh:Genetics Simulated annealing Nucleic Acid Conformation RNA Thermodynamics Algorithm Algorithms 020602 bioinformatics Biotechnology |
| Zdroj: | BMC Genomics, Vol 20, Iss S13, Pp 1-13 (2019) BMC Genomics |
| ISSN: | 1471-2164 |
| Popis: | Background RNA pseudoknot structures play an important role in biological processes. However, existing RNA secondary structure prediction algorithms cannot predict the pseudoknot structure efficiently. Although random matching can improve the number of base pairs, these non-consecutive base pairs cannot make contributions to reduce the free energy. Result In order to improve the efficiency of searching procedure, our algorithm take consecutive base pairs as the basic components. Firstly, our algorithm calculates and archive all the consecutive base pairs in triplet data structure, if the number of consecutive base pairs is greater than given minimum stem length. Secondly, the annealing schedule is adapted to select the optimal solution that has minimum free energy. Finally, the proposed algorithm is evaluated with the real instances in PseudoBase. Conclusion The experimental results have been demonstrated to provide a competitive and oftentimes better performance when compared against some chosen state-of-the-art RNA structure prediction algorithms. |
| Databáze: | OpenAIRE |
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